GC-MS limitations leading to misidentification of peaks?

If two chemical entities co-elute and give fragments of similar mw, you can't distinguish them.

GC - MS techniques quite often rely on the MS to resolve a very slight separation in the GC . If two components result in similar ions, it can be very tricky to split them - there's a lot less resolution from a single quadrupole than the manufacturers claim, and soft ionisation is not easy to fine tune.

You can sometimes get resolution by comparing the small fragments, but that does require very high sensitivity to get meaningful results.

Anybody that says that is angling for someone to buy him a double quadrupole detector or new software.