Hopper Minecart running along rails randomly picks a dead spot where it won't pass no matter how hard you try to push it past it. It can however go in the opposite direction if pushed the other way. The location is random too, I have 2 rail system set up in the same configuration (with powered rails and redstone blocks underneath) side by side and the minecart stops hits this invisible wall in different spots. 

My set up has 3 rows running side by side for each rail system (with redstone block and powered rails at the end to ensure the minecart can bounce back) 

Also note that this is all within the same chunk (running under a bamboo farm if that helps)