Last year, I did a lot of buying on Goodwill. And while I've had some fantastic finds - the coal tender and passenger car from Emerald Night, some HP sets (complete), Boeing 787 (10177), NIB Santa Fe Super Chief - I've also been burned a few times as well. I've got a Friends Summer Riding Camp that's missing two whole bags (everything else is sealed). I've got a Darkseid Invasion missing an entire bag (everything is sealed). I had an Indiana Jones set that was advertised as "complete!" with no picture of the contents. Got it home, and it was $5 of Lego junk.
Darkseid Invasion, I'm going to order the parts I'm missing. It's obvious it was a salvage/damaged box, and that one of the bags was swiped or fell out of a hold in the box. Fortunately, it's only part of the ship, and not the minifigs (which is what's important to me). The Summer Riding Camp, I'm just going to inventory, and eventually order the missing parts.
Indiana Jones, I actually wrote them a letter, and told them how badly what was described differed from what was sent to me. They were fine with that, asked me to send it back, paid the postage to send it back, and refunded me my entire amount.
It's up to you what to do. If they didn't list it as glued, and they have pictures of it out, it's reasonable to say that it's not as described. I get that they sell it "as is", but, there's also an expectation that you, as a consumer, would be getting Lego blocks, not glued Lego blocks. It's a bit inherent in the product. They have a responsibility, as a sell, to accurately describe, to the best of their ability, what they are selling.
It's reasonable to say that they might not be aware that a bag is missing, or parts are missing from bags. But if they've handled the product, and put it on display for pictures, knowing that it's Lego (and yes, Goodwills are quite knowledgeable that Lego are valuable), then they owe it to you to make it right.
In my mind, it's a little different than eBay, since the one holding the auction is the seller. They certainly rake in the dough - they overcharge (IMO) on shipping, and adding in a handling fee is really pretty ridiculous.
It's ultimately up to you, though. It depends on how much you spent. $20? Eh, oh well. The money is going to a good cause. Over $50? If most of it is not salvageable, then you should consider contacting them.