Sure, but it's also expected that it should provide output that could be compiled to produce the input, and in this case it's impossible to satisfy both those constraints. The best thing would probably be to leave a comment in the generated source code explaining the problem, and provide an option to rename overlapping functions.
It's not necessary always possible to output valid-to-compile Java sources. If the bytecode came from a different JVM language, then there are times where javac can't emit certain bytecode patterns.
I would argue that decompilers are primarily reference tools (i.e., a more readable disassembly). It is wrong to see them as source code recovery tools because they will never be able to capture every aspect of the original program. So it doesn't make sense to have as a primary goal the ability to provide output that can be compiled again. It is more important that they more faithfully represent the disassembly.