I have found rather annoying that when I try to draw on a surface it will snap to guides and actually be ON TOP of the guides. Oddly enough, sometimes this happens to where it then draws on the guide, not on the surface and sometimes it draws on the surface.
I am having a hell of a time putting windows in a building I am working on. I’d be more than happy to upload the skp file except that it’s almost 700 megs and guessing people wouldn’t be happy about that. And since my computer is built for doing insane graphics processing and such and still takes minutes to load the file. And takes a bit after every single action. This is even with everything hidden except the actual walls of the building.
However, I am having this issue and it’s damned annoying. I spent quite literally HOURS and HOURS getting some of the doors to cut through some of the walls. Sometimes having to actually destroy the walls, make the door opening and then build up the wall around the door.
I can make a rectangle on the green plane. Push it through to 4.5" so I have a correctly thick wall. Draw a rectangle on it and cut out the door. Sometimes. Other times I do exactly the same thing, and it looks like the above picture as far as the rectangle (for the window or door) is obviously on a different plane than the wall. OR, if it isn’t, I make it, go to push it through and it will NOT. Either it will not push ALL the way through (far wall piece is somehow on a NOT same plane (green)) or the starting side isn’t. Even though it was drawn on it.
I have drawn a rectangle on a plane, then drawn a rectangle for a window/door and when I select inside it to push it out the entire wall is selected. Meaning the window/door is NOT on the same plane. But there is no reason it shouldn’t be. Start and finish said “on surface” when I drew it. OR, now that solid rectangle I created as the wall to start with is in many segments. IE, I click on it and it’s now selecting as many triangles. WTF???
A model that should have taken me a day or two to finish has taken me weeks. Because I have been dealing with these segmented walls. Not kidding when I say that literally one door took me about 9 hours to finally make it. The wall around it (was going around a window and a door) had to be created in like 9 parts. Sometimes I could erase the lines between the parts and sometimes I could not. Having to hide them instead.
I can post some pics if I need to make this more clear…but guessing most others have seen this at some time since I see it all the time and have for years. Just never had a project this important that I felt the need to inquire about it. But this project is so large (in scope and file size) and with only a few windows standing between me and it being finished I find I must ask…WTF??? 
And yes, to put all the info out there…I have double checked every rectangle for placement and plane as I made them. Just to be sure… As I found the ‘snapping’ issue way back when I started this that was making some walls NOT on the correct plane.