Hi there.
You've no doubt run across people referencing Standard Troubleshooting when dealing with end-user issues with mods, particularily when trying to figure out what the hell is breaking one's game when they have a pretty full LO. I'm going to explain exactly what i mean by Standard Troubleshooting and leave this here so other people can add their thoughts and suggestions to it. This is largely written for mod-users and not modders themselves, because mod problems are the things we deal with normally.
Step 1: Identify the problem
You will need to figure out exactly what the problem is. most of the time, it will be fairly easy to figure out, but in some cases the problems will appear to be weird and archaic, such as crashes when entering cells. if you can narrow down the problem as much as possible, it will make finding solutions easier. This is going to require observing the problem in game until you can figure out exactly when and where it happened and what else was happening. screenshots may help.
Step 2: isolate the Problem.
you need to find out exactly where the issue is, and we're going to start by isolating the mod where the problem is. there's essentially two methods for doing this: inductive and deductive. you will note that neither of these issues deals with logic in regards to when mods were added to your LO, because you may just discover that the issue you're suddenly having has nothing to do with the last thing you did and may, in fact, be a pre-existing problem that either you didn't notice or wasn't as prevalent before now. Please note that these methods accept that mods may in fact cause problems that you are unaware of, because that is true. don't assume a mod that says it only deals with one thing in fact only deals with that thing.
Deductive
This method's the simplest, but is going to lean more towards the bottom of your LO for where the issue is than inductive. What you're going to do is disable mods starting from the bottom until the problem no longer exists. You may do this in batches (like 5 at a time) or singly, depending on how much time you're willing to use for this. When the problem is no longer present, then you've found where the problem lies. if you're batch disabling, then you'll have to enable the last batch to disable down to the problem.
Inductive
This method takes more time, but will churn out results faster towards the top of your LO. The other bonus is that you'll figure out much quicker if it's something that's happening in vanilla or not. What you're going to do is disable all your mods down to Vanilla (for TTW, that's FNV + DLC, Fo3 + DLC, and TTW). then enable mods starting from the top and working your way down. You will need to keep in mind dependencies of the mods as you enable them so as to avoid other wonky things from happening in your game (compat patches and other things may be troublesome and not having them enabled may cause unrelated problems). Do this until the problem happens, and then you'll know where the problem is.
if the problem appears to be happening in vanilla, you may want to also check online sources for other people having the same issue, and keep in mind any mods you've loaded that do not have plugins -- texture and mesh mods, ENBs, utilities, etc.
Step 4: Fix the Problem
Fixing the problem, in this case, does not mean "learn to mod and fix the problem", although i can't say that would be a bad thing. However, not everyone has the resources, ability, or inclination to mod, so here's what to do in that case: Search for solutions. Use google or whatever search system you'd like to see if other people are also reporting your problem and see if solutions have come up in response to these things. If nothing comes up, then you might not be able to fix the problem, move on to the next step.
Step 4: Report the Problem
You will notice that Report the Problem is step 4. Reporting a problem without trying to figure out what it is or where it is will be largely useless, especially if you're reporting it to modders who aren't dealing with where the problem is or what it is. also, keep in mind that the problem may not be just in that mod, it may be in a conflict. You will want to contact the mod author or the comment section of the release of the mod and alert them to the problem and see if there's any way to fix it. Regardless of the response, I am unaware of any author that doesn't want to know when things in their mod have gone pear-shaped, so you're doing a good thing. if you get demandy, impatient, and ego-centric, you're likely to just annoy people.