Context would help.
"end up" - finish.
"with you" In some way the speaker was paired with "you". Connected to "you". Assigned to "you".
The suggestion ios that this is less than desirable, unwnated, not their first choice, they didn't want "you".
Everyone had to work in pairs. Why do I always end up paired to you? Why do I always end up with you?
We both like the idea of dating others, but in the end, I end up with you.
Some questions just don't seem to get anyone to answer them. So, you end up with me.