Point Glitch for Deponia, Memoria and The Night of the Rabbit (they cost currently more points)

It's not something that can really be fixed on this end as price information is taken from the Steam API. The same happens with videos which always list the rental price where available rather than the purchase price.

This has been happening for years and it doesn't seem like anything will be done. The CV will go back to normal when the sale ends.

Edit: At least it's only $40 this time, I think it usually makes the games $100.

As noted by others, it can't be fixed through SG, since that's the only value Steam reports games at (and there's no way for SG to effectively apply workarounds for such games). You can see that it's on Steam's end via search results, wishlist, etc; Steam determines price by page, using the lowest value on that page. The associated retail value to that sale price just gets dragged along for the ride (because, y'know. Valve).
Similarly, Free Weekends report their associated games at 0CV. There's a lot of other issues with the Steam system and Steam API (another notable one being that Steam doesn't send out ownership data on DLCs), none of which can be addressed on SG's end of things.

Also, as an FYI, when considering site bugs, searching the bug subforum can usually get you a quick answer, for anything that seems like it'd be noticeable enough to have been addressed in the past. Just, if you didn't notice the search box up in the top left, or realize it could be applied to specific sub-forums. Alternatively, you can search the forums through google by appending "site:Steamgifts.com" to the end of your search.

it is a disadvantage for users who enter/entered during the time of the offer for the bundle.

It really isn't, though. The CV value remains the same as for any other giveaway of the game, so there's no loss there, and entry odds seem to significantly improve for Daedelic games whenever the point values get bumped up. Likewise, you're deciding the specific giveaway is worth the current inflated entry cost, and you're paying the same entry cost as any other entrant. In most circumstances, there's no unfairness or disadvantage to the situation, from any angle.