I'm new to the HVAC business and I'm a bit curious as I'm looking over some drawings I just sent out and noticed some lighting conflicts (only 4" of clearance for some flourescent lights)
In general, the contractor is likely to issue an RFI (request for information) to you, the designer, to figure out the solution. Unless it is design-build, contractors usually accept no responsibility for resolving conflicts in the bid documents. Unless they can get paid for it.
It is important to bring your findings to someones attention ASAP. The sooner that the problems are addressed the cheaper the solution (possibly). It's easier to drop a ceiling or soffit before it's installed then after.