> "Researchers recently discovered that the proton sometimes includes a charm quark and charm antiquark, colossal particles that are each heavier than the proton itself."
You articulated my feeling better than I could. Surely this is something the researchers have accounted for and there's a good explanation (whether I can actually understand it is another story)
It's explained better here.
tl;dr; is that they are virtual particles and don't have the same mass as a "real" charm quark.
Another weird thing are virtual particles that can popup without energy. They are similar to real energetic particles in a sense that they are manifestation of the same quantum field (for example charm quark field) but they are different from real particles because they don't carry energy and thus can't live long.
World is very weird. Math works though.
Proton is just a weird ball of bubbling energy that stays in one place because up quark and down quark quantum fields got "stuck" together there through complicated colored strong force. But there's so much energy there that wants to get free but can't that there are constantly things popping in and out of existence.