i had a box mod that trashed my protected 14500's. was too tight a fit and prying it out repeatedly to charge it ruined it. the protection circuit was hosed according to an electrician friend, so i chucked them and have no plans to use anything with a 14500 again.
one thing about mods and battery clearances is, they can be a ..... to deal with.
This is the first I have heard of this problem with 14500s. I have used two Bartlebies (3.7V box mods) for 6 months now without any issues to the batt at all, and they do fit tight in the box. When I remove the back to get the batt out, I
gently pry it out with the corner of the back-piece. I have used the same 4 14500 batts with a charger for the whole time without any problems.
My guess is your box mod was too tight, which is possible. They are often tight. How you pry it out is important too. I would not use a screw driver, for instance. And I would certainly not discount all PVs that use the 14500, or the 14500 itself. That's like saying that the contacts in my TV remote are not good, so I am never using a device that uses AA batteries again. That would be a bit over-reacting, and there are very good reasons why 14500 batt mods are so popular.