It comes down to what is taught in Poland about the Polish–Lithuanian Commonwealth. The Union of Lublin isn't shown as unfavorable for Lithuania as it really was. A lot of the southern territories of the Grand Duchy of Lithuania was "given" to Poland but it was actually stolen by Poles, the Polish language overpowered the Lithuanian one among the elites, the common coin was Polish-based. At one point, the PLC starts to get treated like one big country, with Vilnus as one of the major cities of Poland. The Vilnius University shown as an important Polish university, Mickiewicz calling Lithuania his home while writing in Polish, etc. The whole stuff after the World War One is barely touched in the high school when barely anyone cares about history anyway, I guess most people don't even know it. With this lack of the knowledge, Vilnus is one of the lost Polish cities, just like Lviv.
The current animosities are down to the early 2010s and Grybauskaitė being the president of Lithuania - when there was the increase of the Lithuanian subjects taught in the Polish schools, troubles with Polish surnames, places' and streets' names. The Polish hooligans were also quick to pick it up. To be honest, Lithuania isn't looked down at but people don't understand why Lithuania has the right not to like Poland.