I think it comes down to people playing fallout4 and expecting shooting to work well. As in, well, compared to other games where you shoot guns. Skyrim doesn't have any guns, so the fact the engine doesn't do shooting that well doesn't matter.
That said skyrim's archery is probably the best in the series, and woe be tide to anyone who tries to be an archer in morrowind. The glitchy combat doesn't seem to come up or matter in skyrim, because no one expected the combat to be any good in the first place. Although on top of that I do think obsidian's writing in FNV shows up the writing in FO4, I found myself starting to find FO4 dull. However part of the dullness of FO4 is the radiant quest system from skyrim being cranked up to 11, in skyrim you rarely got radiant quests, but in fallout4 you can have a dozen at once, and early on even. Radiant quests are shit, because they have LITERALLY no writing. On top of that hoovering in fo4 is something that starts to feel mandatory, but then weight limits. In skyrim you pickup stuff you like, because honestly, you don't really need any of it, and so the scavenger hunt doesn't become a burdensome aspect of play.
On top on top on top of that, fo4 isn't really an upgrade on skyrim, and yet came out many years later. Witcher3 for example. Skyrim was ahead in the calendar. However things like witcher3 and the new wolfenstein (1st one not recent one) were out in time to compete for people's memories when fo4 rolled around. Now ubisoft makes an open world game 5 times a year. But in skyrim's day the formula still seemed "fresh".
TL;DR;
No they don't at all in anyway share the same problems. Who told you that?
Yes, the mistakes made in both games are the same mistakes by the same people, but the expectations, context, competition, and order of release date changes drastically how one might view the game.