It happens when you go into soft, lagless landing (0 frame landing) instead of the 4 frame empty landing, which you can do by just boosting really low to the ground, like jumping and insta-boosting or by running offstage and insta-boosting back on. The 4 frame empty landing gives boosts back by itself, but the soft landing is lagless and doesn't have any frames that it could give boosts back, so if you immediately follow it up with something that doesn't give boosts back (like shielding or a perfectly timed dash), and then go airborne somehow, you don't get boosts back because you never went through a landing animation.
Best way to fix it would be to make every grounded animation give boosts back. Including all attacks if they don't already (you could soft land, instantly attack, then get hit off before idle animation gives boosts back), shielding, running/walking if they don't already, the teeter animation, and even the platform drop through animation (you can soft land on platforms and fall through the next frame) and probably a few other things I haven't thought of.