There's a lot of variance in the results for how well you do as a caller in 3-bet spots, so you really need very large sample sizes to draw firm conclusions. Your aim is to lose less than you would by just folding to the 3-bet, so
over this sample, you'd literally have done better by doing just that (folding), but many of the "standard" calls vs 3-bets are extremely close to breakeven. It's not as if you're fist-pump calling when villain 3-bets and you have KQs. You're just trying to win enough pots to break even. Since the hands are so close to breakeven, with a little bit of runbad you'll be -EV, and with some rungood you'll be +EV.
When analysing your database, I would pay close attention to whether you are in position or OOP. It's extremely hard to play hands like KQs, QJs, JTs when OOP vs a 3-bettor, but you should do fine in the long run if you are
in positon (e.g. on the button vs SB), provided you don't overplay your hand. Have a look at (or even post on the forum) some of the hands where you called a 3-bet with the hands that have been troubling you. Were the big pots all coolers, or did you make silly bluffs, or bad call downs?
FWIW, I just ran the "called 3-bet" filter on a similar sized database, and my heat map is a horror show. (My EV was about -2.75bb, but I actually lost much more than that due to runbad in all in spots).
But note the sample size. I only called 3-bets 179 times in about 80,000 hands, so some of the suited connectors were only in that spot 3 or 4 times (and it seems I never had T9s a single time in such a spot. #Variance). You can't generalize based on such minute sample sizes.
(I have no idea why I apparently called 3-bets with K7o and A4o. It might have been when I was shoved on by someone with a 7bb stack or something ridiculous like that).
P.S. If your opponents have very tight/strong 3-betting ranges, you can and indeed should, fold more often. You won't get "exploited" by over-folding, because they won't adjust. In fact, you would be exploiting your nitty opponents by not paying them off.