Are you saying if you pull of the air filter cover or "dogbowl" off and remove the air filter element, there are bugs inside the housing? Just trying to understand exactly what you are telling us. If that's the case how long did the bike sit before you purchased it? That's where I would tend to think they came from.
I would clean them out and if the bike runs properly, not worry about them again.
Lastly, go buy yourself a service manual for it. You can find both printed and downloadable copies online. You will find it invaluable.
2006 V-Star 1100 Classic
Silverado windshield and passing lamps
OE Highway bar with custom mounting brackets
Kuryakyn Dually ISO Highways pegs
Barons Nasty Boy Slip-ons
Kuryakyn led headlight halo