Majority of the issues I've run across so far are 1 of 3 things:
1 - Different addons re-positioning the same windows without clearing anchors first (these are collisions, and all parties should code around them)
2 - A single addon re-positioning windows without clearing anchors, or simply setting too many duplicate anchors (these I call bugs)
3 - Too many addons with large sets of menu options on their top-level panels in the Settings Menu ( and let's face it, they all use LAM )
1 & 2 should be fixed by the individual authors whenever they can figure it out, and since #1 is an everchanging landscape I don't foresee this issue truly going away permanently. Let's face it, we can't predict what addons users will and won't use.
3 I have a workaround that I think alleviates the issue somewhat and it's in the latest version of the 5 addons I uploaded today which all embed the new LibWykkydFactory (which I will be uploading independently later on). Submenus. It is a "hack" but it works wonders. If you're an author you should go check it out