Was the 1939 Red Army more disciplined / better behaved than the 1943-1945 Red Army?

There is a certain opinion-based element in how the question is framed. This answer will refrain from evaluating the "better" aspects, and focus instead on what is known: regarding the events in the "territories formerly known as Poland" that 'requested' to join the Soviet Union after they were liberated from being Polish. That is in the 196,000 square kilometers or about 51% of the territory that belonged to the Second Republic of Poland, together with a 1939 population of 14.6 million inhabitants – of which 6.17 million were ethnic Poles.

Anything that did happen in these territories before the Germans took them when invading the Soviet Union was kept under wraps by the Soviets. When the Germans discovered some of these facts, they seized on that for their own propaganda. Unfortunately that made these infos quite tainted in the eyes of many. So much so, that the Soviets could at Nuremberg claim unopposed that Katyn had been a German crime. That was then post-war the official Warsaw pact line. They didn't want the matter discussed, especially not in Poland, and if it did surface somehow they just blamed all on the Nazis. That is one big reason for why there was little research into this until the 1980s.

Since the Soviet Union immediately annexed Eastern Poland in 1939, and granted Soviet citizenship to all inhabitants, any crimes or misdeeds would technically be towards their own citzens.

After annexation the Rasnaya Zvezda (Red Star newspaper, offical organ of the Red Army) reported that of the Polish Army 190,584 prisoners were taken by the Soviet side. Of these 130,633 left a trace in the form of being listed later as Prisoners of War. Whether both numbers are entirely accurate may be debatable, but it shows that around 50,000 of them disappeared somehow. The lower number includes 457 people listed offically as "died in NKVD custody".

To get a better glimpse of some 'irregularities':

Immediately following the Red Army's entry, the occupied territories also experienced, to greater and lesser degrees, episodes of anarchy that coincided with the first wave of state-orchestrated repression.

During this period individual soldiers togetherwith entire units of the Red Army, and Ukrainian nationalist elements as well as common criminals (those seeking the opportunity to simply enrich themselves through the misery of others), were involved in a variety of assaults, murders and executions of Poles.

Typically, victims were members of wealthier classes (landowners as well as their families), military and civilian settlers, and intellectuals (for example: teachers), local and national government employees, officers and enlisted personnel of the Border Defense Corps, regular police, and such.

The bloodiest episodes of anti-Polish violence occurred in Grodno, Wolkowysk, Swislocz, Oszmiana, Molodeczno, Chodorow, Nowogrodek, Sarny, Kosow Poleski, Zloczow, Rohatyn, and Tarnopol. It must be acknowledged outright that even an approximate number of those murdered, shot or executed is unknown.

Two principal motives lie behind this initialwave of repression: first, to frighten the public at large and eliminate intellectual, political and economic elites who represented potential adversaries of the Soviet regime; and secondly, personal aggrandizement or enrichment which simply entailed seizure of possessions and assets.

Soviet assimilation essentially amounted to eliminating entire social and political groups thatwere deemed inimical to the new order. In the final analysis, this process of gutting Polish society on the part of the Soviet regime was an absolute prerequisite for assimilating the vast expanse of territory it had seized. The targeted groups included large landowners, along with the strata of management who maintained the estates; bourgeoisie, that is, individual homeowners, entrepreneurs, merchants, and at times even skilled tradesmen and artisans; and those associated with the Polish state: veteran land-grant holders, police, military and forest service personnel, employees of the local and national government, as well as activists connected with various political parties.

Members of each of the aforementioned groups were subject to systematic eradication, a process often beginning with staged robberies and murders followed by confiscation of personal property or banning one from professional practice. This normally culminated with arrest and deportation deep intoRussia. And while the peasantry may be said to have gained an immediate advantage as a result of the misfortunes of the propertied classes, those advantages were short-lived. In fact, most were never able to begin the following year's spring planting. Almost immediately following the distribution of approximately 25 percent of expropriated land in the fall of 1939, a program of forced collectivization was implemented the following year under the kolkhoz and sovchoz system. Thus, the initial land transfers amounted to little more than a propaganda exercise for the Soviets in terms of class warfare rubric.

– Marek Tuszynski & Dale F. Denda: "Soviet War Crimes Against Poland During The Second World War And Its Aftermath: A Review Of The Factual Record And Outstanding Questions", The Polish Review, Vol. 44, No. 2 (1999), pp. 183-216.

The above is a bit tainted by being written from a very anticommunist nationalist Polish angle that emerged after Poland 'went West' after 1991, but despite that bias it's god point of entry into the issue.

If it should still be desirable: For how to evaluate the "better" angle from the question it should be factored in that:

• Ukrainian hatred towards Poles was one main driver for 'private action' of some in that region
• The Polish-Soviet war from the 1920s not as atrocious as German invasion into Soviet Union and longer ago than the latter. 'Revenge' less acute a motivational feeling than when Red Army moved towards Berlin
• The whole fighting was over for the Soviets in a minimal amount of time. The German invasion of Poland is always named "Blitzkrieg", yet the Soviets had much less to do when they attacked Poland from the East.

As for the "Discipline" aspect:

To counteract a tidal wave of discipline problems the army enacted the Disciplinary Code of 1940. The rewritten definition of military discipline in 1940 made no mention of socialism or social-political duties. Instead, the army stressed unquestioning obedience to superiors and referred to Lenin’s admonishment that, “Without discipline there is no army.”

In a campaign to bolster discipline military tribunals handed down stiffer sentences in 1939 and 1940. In 1939 the army executed 112 officers and men for their crimes and in 1940, 528. In 1940, 12,000 officers and soldiers were sentenced to serve in penal battalions. In 1939, military tribunals sentenced 2,283 servicemen to from three to five years in prison, and 17,000 in 1940. The number of men given more than five years in prison for their misdeeds also drastically increased in 1940 to 7,733 from only 812 in 1937.
_{— Roger R. Reese: "The Soviet Military Experience. A History of the Soviet Army, 1917–1991", Routledge: London, New York, 2000.}

Since the question shifted its focus on rapes:

Both women and men suspected of violating Soviet law were dealt with harshly: arrested, brutally interrogated, incarcerated in prisons, and sent to forced labour camps in the USSR, the infamous Gulag. Like the Nazis in western and central Poland, the Soviets aimed to completely transform the society of eastern Poland, by obliterating not just the military force, political power, and economic system of the Poles, but also their culture and values. They thus viewed women as real or anticipated enemies, too.

Males in eastern Poland were also arrested and incarcerated at a much greater rate than women, approximately nine to one. Women ended up in Soviet prisons and camps for attempting to cross the Polish borders, belonging to a resistance organization, or refusing to accept a Soviet passport. Once arrested, they were tortured and given the same sentences to the same hard labor as men. But they were also victimized as women: the NKVD subjected them to humiliating baths in front of male staff, gynecological searches, and sexual abuse.
_{— Katherine R. Jolluck: "Women in the Crosshairs: Violence Against Women during the Second World War", Australian Journal of Politics and History: Volume 62, Number 4, 2016, pp.514-528.}

More personal accounts of cases of rape, including a sometimes wide ranging allegation on the level of "they were all raped" to be read in:
— Katherine R. Jolluck: " Exile and Identity: Polish Women in the Soviet Union During World War II", University of Pittsbrugh Press: Pittsburgh, 2002, pp.153–75. (example)