While Bethesda is famous for its Fallout franchise because of the gameplay and lore, a lot of players can also tell you the same thing, which is that the studio's games are buggy. It can get quite annoying and even interfere with progression. A lot of things can cause it, and here are some that might be fixable.
1. You Have Too Many Mods
The game can only take so many changes before it begins to malfunction, and having too many mods in Fallout 4 will definitely cause it to be buggy. It can slow the game down or the mods will not function as intended.
Worst case scenario, it will make the game crash often, which can be very annoying. Having a lot of active mods also increases the chances of having incompatible mods. These usually cause issues when you execute them for specific actions.
2. Corrupted Game Files
The use of mods doesn't just risk the game being overloaded. In some cases, it can also corrupt game files that make your saves unplayable. Try to turn off certain mods to see if everything returns to normal after you do.
If you reach the point of the game being vanilla and the game still keeps crashing, then it might really just be a corrupted game save without mods causing it. Unfortunately, there's not much you can do and you'll have to load the latest uncorrupted save.
3. Operating Below Required Specs
Fallout 4 is a relatively old game as it was released in 2015. Even so, the game can be demanding on your device, whether it's a console or a PC. To be on the safe side for PC, you should have at least 8 GB RAM, 30 GB of free space, and the equivalent of an NVIDIA GTX 550 Ti GPU.
If you want to have smoother framerates and decent graphics, you'll need better equipment with requirements like 8 GB RAM, an NVIDIA GTX 780 3GB equivalent, and an AMD FX-9590 4.7 equivalent. Otherwise, you might want to lower some settings to keep it from lagging or crashing.
4. Overdoing Glitches
There are some popular glitches within the game that allow players to forgo mods. For instance, there's a bottle caps glitch that basically leads to unlimited currency. The same goes for the settlement size, where players can use the gun glitch.
In case you don't know, storing guns in the workshop inventory decreases the meter of your settlement size, letting you add more structures and items than the game allows. This meter, however, is there for a reason, as exceeding it would bog the game down.
5. In-Game Issues
When you've done everything and the bugs seem to still be there, it could really just be from a malfunction in the game, and there's not much you can do about it but try workarounds. There are plenty of sources online where you can look for specific answers.
If you can't get through a mission because of a glitch, for example, chances are someone already went through the same thing and found a way to make it work anyway. Look for answers in places like Reddit to see if someone has the answers to your problems.