Interestingly, I've only been noticing this problem for the first time in the past few days! Sometimes it takes several jumps, and it only seems to be with iMG quoins.
I think it's not that the quoins require multiple jumps, but that it takes the game a while to notice you've collected them -- sometimes I run all around jumping through quoins that remain steadfastly in place, then all at once poppoppop they disappear and reward me.