This is a prime example where lack of knowledge on the part of the electrical contractor has led to problems. Please spread the word that there is a BUILDING code out there, and the electrical code is subservient to it! The integrity of fire partitions is much more important than "neat and workmanlike", as is the integrity of all structural members of the building.
SPREAD THE WORD: THINK AHEAD
Check with the engineer or the inspector prior to drilling any engineered truss or lumber, seal all penetrations you make through fire rated partitions, and never assume your work is the only trade in the building.
About your problem:
There may be an allowed size and number of openings or compressed points on the fire barrier you have compromised. Or, there may be a fix for the problem you have created. The manufacturer and/or the engineer will have the answers to these questions.
Earl
