Hi
The first place to start is to ask what program the other guy used to generate the gerbers and the drill files. Often the solution is a switch setting on your end to make it "Stupid Program A" compatible. The root cause is related to a whole world of people working with a set of standards that are only loosely defined.
Once you know what program does what, there often are things embedded in the comments on the files that will let you automate the switching process.
There are a few dozen other things that could be going on, but that's where I would start.
Bob