Minecarts are (and have been as long as I can remember) way too unreliable. They stop when they shouldn't, and have a tendency to slip off of their intended tracks. This makes using them for collection (minecart hoppers) extremely frustrating. Every time I log into my server, I have to crawl under my farms that use them to find where it's stuck, break the minecart, recraft, then replace on the proper track.
This has got to be one of the oldest bugs in MC, yet I couldn't find any bug reports upon searching.
What exactly is your issue?