Train services aren’t great in that part of the world. But if you know a train is running, you can add it to the app manually. (Just run a search from anywhere to anywhere, and in the results scroll down to ‘add manually’.)

I found that buses were much better way to get from Tallinn-Riga-Vilnius.

Seat61 has some good advice for

Warsaw-Vilnius https://www.seat61.com/trains-and-routes/warsaw-to-vilnius-by-train.htm

Vilnius-Riga https://www.seat61.com/trains-and-routes/vilnius-to-riga-by-train.htm

Riga-Tallinn https://www.seat61.com/trains-and-routes/riga-to-tallinn-by-train.htm

Note that although he says there are no international trains between Lithuania and Latvia, there is supposed to be a new direct service starting in December.