loose wire?? or perhaps the speaker is out of phase....as in positive is on negative instead and vice versa!? Are they amped or running directly from the head unit? if directly from head unit, then possibly a fault with a loose/tempramental wire. failing that..whilst the speakers are on and working..push the crackling one down from the cone with your hand and check to hear if it continues to crackle then? if it stops and is sounding relatively clean..within reason as your hand is on it..then it may just be a problem with that speaker!
Try switching the 2 pos and neg wires from one 6x9 speaker to the other and see if the problem happens with the other good sounding speaker...if so..then definate wiring issue. if it sounds ok..then the other initial bad sounding speaker has gone faulty! Hope that helps!