I've had problems with my autosiphon on multiple occasions (even having to basically hand pump half my beer on my 1st batch) and each time my beer has turned out fine. It takes a ton of oxygen to oxidize beer. I wouldn't worry about it.
The black cap is the anti-sediment tip. I didn't realize this either in the beginning. Before I knew this I used to wrap clean/sanitized muslin bag around the end of my siphon to try to filter out stuff. Very bad idea! The seams of the bag would stuck get stuck and stop the siphon constantly.