Some tunnel to tunnel intrusions are actually not such, as only the outer part of the tunnel (of which has thickness) intrudes, not the inner envelope. In addition, intrusions must occur with catwalks and the station in order for them to appear realistic. Anything that doesn't intrude the tunnel more than the catwalks/station are generally safe.
That said, a lot of tunnel testers (at least in the past) lack any basic common sense. A slight intrusion into the lower corner of the tunnel is safe if it doesn't stick in very far. (This is because the train's wheel assemblies aren't going to grow arms.) The entire track must be simultaneously tunneled for the test to be consistent.
My current avatar is satirical of those who make improper tunnel tests.