Looked around the forums and hadn't seen an answer or a rules clarification:

An opponent of mine had Wedge/Biggs/Kyle + moldy crow + recon specialist. So now for three or more turns he has them all focus. Now for each of those turns he has Kyle place a token on either of them (not both). The problem came during clean up phase, he said that he only had to remove one focus token from Wedge or Biggs at the end of each turn. That means Biggs and Wedge were building up focus tokens too (mostly Biggs).

Was he mistaken? Not sure who is correct here. Please help.

Very much mistaken. Only focii assigned to the Moldy Crow herself are indefatigable.

All tokens clear (except target locks) after the end phase. Moldy crow only allows the HWK to keep the focus tokens. Kyle's ability allows the passing of focus tokens not keeping focus tokens.

All tokens except TL, ion, cloak, and energy tokens are removed in the clean up of the end phase.

That makes me feel better then. Thanks all.

Page 13, End Phase:

To add to this, I think there is a subtle hint in the colors that FFG chose for their tokens. You remove all the green ones in the End phase.