Yes, if you were expecting to automatically disassemble the entire ROM at once, it won't happen. The ROMs contain code and data. Disassemblers can only assume everything is code. Once it hits data, the disassembly is going to be incorrect as it tries to disassemble code that's not code, and may or may not line back up with the actual ASM code.
The only disassemblies that have been done are by hand, by people who took probably many hours manually separating the actual ASM code from the data. (and even those were from comparatively small early NES games. Early games that didn't have memory mappers to complicate things.
Though Disch did some work on Final Fantasy, he was still only able to decompile a few of the banks as I recall and not quite the entire game.)
I did a little work on a couple NES games, but it was tedious work copying blocks from FCEUX and then trying to figure out what the code does.