it is working as intended.
the difference is that swift only takes regular enhancements for running and flying; i.e. SOs (single origin) or IO (invention origin) generic enhancements. it is deliberatly limited in this way. ONLY regular enhancements.
as Captain Fabulous points out, sprint specifically takes regular AND set enhancements, ones that enhance running speed and/or jump. it states that it ONLY enhances running speed/jump, while taking regular running/jumping enchancements, and sets that enhance running/jumping. NOT flying sets.
i think the GM was simply stating that they do not know why that it is that way, but you can, and did, submit a bug report. but, as happens often with me, it gets pointed out that this is WAI, that this is the way it is supposed to work. it's a 20+ year old game, it's riddled with strange things that sometimes make no sense. but it does say in the power description that it takes enhancements, that is to say regular ones. it does not say that it accepts set enhancements.
what it says on the box is what it means. you may disagree with it, but it is not a typo nor a bug. it's a feature, not a bug. that is how it is meant to work. they designed it that way, and it is not misleading, it is pretty straight forward. regular enhancements only, no set enhancements.