This is obviously a well-known phenomenon in software engineering and I don't think anyone here is going to be be particularly surprised that it occurs in the aerospace setting. What is a little more surprising, to me at least, is that the systems people over there don't have procedures in place to minimise risks stemming from lack of communication.
It isn't realistic for any sub-team to be fully familiar with the overall system but surely, for instance, if a team is working on component X which interfaces with components Y and Z, then it should be standard practice for the X team to spend at least some time with the Y and Z teams during development?