By the time the beer is in secondary, it's beer: it has alcohol and a pH to not easily contaminate (and when it's in primary, it's expelling so much CO2, it's not getting much oxygen). Having some headspace is OK with beer. As for the OP, yeah, sometimes my secondaries get some bubbles, hops, yeast floaties, or a slight oil slick. It all turns out well...and if I've got floaties, they tend to drop down once I crash cool.
Whatever is on top of the conditioning beer is not much of an indicator of its health: if you're still worried about your beer, taste it! The only time I've had an infected beer, it was quite obvious from the smell/taste. But when it's in a carboy, I've noticed it's pretty hard to get an idea of what the color, much less flavor profile is like (not unless you have some special technique for tasting by not drawing a sample
) I always just guage my beer's maturity by tasting a small sample of it before going on to bottling/kegging.