For me when I notice I have updates in the store and click on it, there will almost ALWAYS be more than what the phone reports. Yes it appears some are being lost in the shuffle. This certainly IS a bug but you have to ask yourself is it "mission critical" That is does it prevent the device from proper operation? I would say no. Yes it can be annoying, but the VERY easy work around is to just check the updates tab in the store every couple days, or whenever your OCD depends. lol
I'm with the others who have said it's not a bother.
