This will have to be solved on site. The obvious answer is holes too large/small or bolts too large/small.

You give no useful information.

Check to see that if tolerance for the holes and for the bolts is in conflict.

For example if the tolerance allows + or - .01 and the bolts are +.01 and the hole is -.01 they will not fit!

Verify:

if tapping tool still in tolerances.

if bolts are within specified tolerances.

if bolts were not deformed during transport.

if bolt introduction is correct and not with an angular error.

if bolts have a surface anti corrosion layer which means that the bolt could have been correctly rolled but the protection layer thickness is not controlled.

Specify the materials!! We need to know that.

Then specify the class of fit. We need to know that.

By all means look into your class of fit like TVP45 said!

Have the clients return the plates with the bolts that will not fit so that you can determine where the problem is.

I would check the tapped holes in the plate with a thread gauge randomly as a part of quality control.

This may not be your problem as they may have problem with the bolts.

I agree with ozzb. If only some bolts don't fit, I would suspect the bolts are the problem, not the tapping.

Seems to me that it could be an issue of pitch misalignment. Have the dimensions of the actual plate verified and compare it with what you've produced. Perhaps the customer provided you with incorrect data or, perhaps your layout is incorrect.

Highly unlikely that the tap is incorrect.

It could be possible some bolts have deformed threads.

A more likely cause is swarf contammination after machining or foreign matter picked up in transit in the threaded holes or on the bolts which can cause binding. check your finishing, storage and shippng proceedures.

Usual practice (if feasible) is to put the connecting bolt on the plates at your end, then you know the problem before the customer tells you. (Tell him, that you will supply them, and the cost to be borne by him)

This will avoid the thread damage and dust contamination, and if you put some antiseize, it is for best. (For our large ones, of course it is either with the fasteners supplied assembled or at least wit a grub screw/ plastic cap in place)