The purpose of making a bashed patch is letting wrye bash "bash" together all the mods, as to try and correct any potential errors/ conflicts between all the mods you have installed. Which it does a pretty decent job of. However, the more mods you install, the more conflicts are likely. I don't know if you did this, but after creating a bashed patch, you really should check the patch with xEdit and check if Wrye Bash kept the functions you wanted/ expect. Go through all the edits in the bashed patch and manually correct things if needed (drag and drop the function you want into the bashed patch). And always place the bashed patch as low as possible, but when using LOOT, it should do this automatically.