Bit of both...
This isn't a rare problem unfortunately, and it always seems to come down to slightly overzealous torquing - or worse, bad calculations in translating from NM measurements to ft-lbs, or using Nm numbers in place of ft-lbs.
The manual specifies:
35 + 4 Nm OR
25 + 3 ft-lbs.
Note some manuals say 24-27 ft-lbs.
Obviously confusing the numbers and doing bolts up to 35-39 ft-lbs is going to do the threads in.
Not as obviously, going to the max torque listed of 39Nm or 28 ft-lbs is too much.
Experience on airheads says that safe torque is 24 ft-lbs or 35 Nm MAX.
A common problem is assuming that slightly tight will be good, so we always torque down to the high end of the range - I did so for years myself. Bad idea. And torquing down in three stages as the manuals suggest is also a VERY good idea as it prevents one bolt from being overtorqued due to the leverage effects of uneven torquing.
Who knows when the bolts were overtorqued, but it's certain that they were. However, knowing why doesn't help much when it's too late.
The fix is fairly simple, but difficult to carry out well. Just use helicoils or inserts, whatever seems appropriate and is available. It is absolutely critical to get them in straight, and also not block the oil passages.
A hand drill aligned by eye with the greatest care and assistance will result in a destroyed engine block - you have been warned.
It must be done with a jig or drill press locked at exactly 90 degrees to the surface. A very long drill bit drilling down through a cylinder bolt hole is possibly a way to do it accurately enough, if it's bolted down with the other three bolts, and a sleeve to hold the drill bit exactly in the centre of the bolt hole at the top.
Use Loctite on the insert or helicoils to ensure they don't back out or loosen. Make sure the inserts are long enough with lots of thread depth - two may be required.
Good luck, and take your time and be careful!!
Seek, and ye shall find.
One world, Two wheels.