Partly recompilation generates invalid address fault?

I'm making an x86 emulator with C++ (currently 8086/80186 with some little unfound errors). When I'm compiling all the files (deleting all *.o files and running make), the emulator runs fine (still some errors, but it runs). When I run make, just having one file adjusted, the emulator (JPCSP, a PSP emulator) gives me an invalid opcode/address fault. The emulator does use some pointers at different places though (mostly dynamic memory and optimization), can this be the cause? Causing addressing errors with partial recompilation using make?
undefined behaviour is undefined.
That's the best guess with the information provided.

> dynamic memory and optimization
encapsulate your memory management (by instance std::vector)
don't preoptimize.
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