One tip I can give is avoid re-reducing images that were already reduced by winreducer or ntlite and always start frmo a fresh base from an officially downloaded ISO + adding the latest updates available manually, but always using a fresh base and not reprocessing a previously winreduced image or ntelited image.
Unfortunately yes, Winreducer does have issues, particularly when removing some components - the OS WILL install, without errors so it appears to work, but later on you will run into issues. Winreducer allows some files / components to be removed that can be essential later on in specific conditions or during an update.
So the best way is probably to only use winreducer or ntelite to apply tweaks, and build own custom scripts to apply post install, to remove unwanted components and trim the fat.
As far as winreducer, when not removing any component and just applying tweaks, the only error I have observed int he CBS are duplicate ownerships errors. This is usually non critical and can be fixed by running sfc - no other corruption or file integrity observed after that - but when using winreducer to remove some drivers/components/other, you will see those more critical errors. even when using protect windows switches or the respective protective switches.
As far as net3.5 could not get it to work with winreducer, it does not integrate properly.
In NTLITE it seems to integrate, BUT when trying to disable it in features I still get an error that base is not present or something similar.
So probably the best way to integrate net35 is post install
DISM /Online /Enable-Feature /FeatureName:NetFx3 /All /LimitAccess /Source:g:\sources\sxs
(replace g with whatever drive letter contains your windows install media.
But even using that method, if you try to DISABLE the feature from turn on/off features, it willg ive you an error and not allow you to disable it, BUT otherwise it works, and have run some net3.5 specific apps successfully. I compared NTLite integrating the .19 update against winreducer, and in NTLite it was flawless. in Winreducer, it integrated it, but the install was messed up, would take several clicks to the start menu icon for it to open up, sometimes stalling completely, sometimes windows stalling completely, even with 0-2% CPU usage, whilst on NTLite it went flawless. I am only but making FACTUAL criticism, not here just to complain and troll. But when you clearly see a developer take offense and try to move unresolved topics as answered and solved, it says a lot.......... One thing where WinReducer shines, is the user interface and the "tweaks" section which has more options that NTLite lacks, if only it was possible to use both without messing up the ISO it would be great.
I am not attacking anybody PERSONALLY here, it's not PERSONAL, it is about my observation on the software itself, and I am glad that at least another person has had the courage to speak up about these issues.
No matter what software you use, you cannot slim down windows without some consequences and side effects - you might get the illusion that everything is fine because the OS installs and is functional, BUT deep inside, there WILL be issues eventually - you might or might not experience those, depending on what you use windows for, but at some point an update might come along the way and "expect" one or more of these components to be present - and if those are not found, the whole update would fail.
This applies to all software, though NTLite seems less forgiving of such things and offers better protection, though not flawless........Unless you are doing GAMING I would recommend leaving all drivers and components as is, and only applying tweaks - then using post scripts instead, along with scripts to reverse changes if needed.