It depends whether or not you are using it in the context of computing language or not:
In non-computing language, or in normal English, "compiled" is used to mean 'put together' e.g.:
We compiled a dictionary.
However, in computing, "compiler" is defined:
(intransitive, computing) To be successfully processed by a compiler into executable code.
A source code would be compiled, in computing language.
So, its the context of the usage. But in either case, they both mean that the files have been made into binary files.
N.B. "We compiled the source files" in normal English could be misunderstood for you putting together the source files, so if I was in a situation outside of computing, I wouldn't use compile in that way.
Hope that helps!