When the Soviet Union came apart, it broke into its 15 constituent union republics. Somewhat similar to the way the United States is made up 50 states, the Union of Soviet Socialist Republics was made up of 15 soviet socialist republics: Russia, Ukraine, Belarus, Estonia, Latvia, Lithuania, Moldova, Armenia, Georgia, Azerbaijan, Kazakhstan, Kyrgyzstan, Turkmenistan, Tajikistan, and Uzbekistan.
When the central government came apart, those union republics all had functioning local governments (somewhat analogous to US governors and state governments), and so the natural thing was for those governments to take things over within their already existing boundaries.
The enclave of Kaliningrad was part of the Russian Republic, separated from the rest of Russia by Lithuania and Poland. There are other such enclaves--the borders between the republics of Central Asia can get messy. But Kaliningrad is the biggest.
SO: it would have been a Very Big Deal for Poland or Lithuania to try to grab that territory, which had a lot of military significance for Russia and was mostly populated by ethnic Russians. The path of least resistance was for Kaliningrad to just stay as part of the Russian Republic despite the geographical separation.