Should this window have caulking along the bottom edge? When I moved in some of them did, some didn't. I caulked a few. Now I am wondering if I did the right thing.

 

Not clear what bottom edge your referring too!

 

right there

 

Yes, that should be caulked along with the rest of the window perimeter.

 

I am asking because I have a water stain on the ceiling, first floor about 6" to the right of the lower left window in this picture. Seems to line up with the top window.. There was no caulking on the sides or top.

 

also, it seems there was water getting in the corner of the inside of the window.

 

You have several potential sources of water besides just the window... starting with the siding.

Your fascia does not overlap the j channel on top and I would guarantee that the top of that j channel is not caulked. So rain can get right behind the siding.

Secondly, water leaks behind the vinyl siding at the bottom corners around every window. This is normal since vinyl siding relies on housewrap and proper methods of flashing to keep that water out. I'm guessing you may not have a WRB (housewrap) behind the siding. If so, this could be a siding issue, not a window issue. The window is just where you eventually see water.

And then 3rd your windows may not be caulked on the outside or your sills underneath the aluminum cladding may be rotted away, allowing water to get right in the wall.

4th, it looks like the butt joint in the siding at that spot may be separated because it looks different than all the others... it looks like a gap rather than a lap.

Hard to tell what the problem is without tearing into it. Removing a piece of vinyl siding below the upper window and looking at that butt joint would probably be number one. Plenty of videos on youtube about how to unzip vinyl siding and how to use a Malco Sideswiper.

 

Here is a top view from the roof do I need to get up there and run a beat of caulking along the top?
It never surprises me to find out things were done wrong on this house everything that's been done to it is half a-ed. Unfortunately I'm not much better.

 

Besides the spots you initially asked about, these are the places I was referring to. Top of the j channel where the yellow meets the white. Everything else is a siding problem that can only be corrected by removing siding or at least peeking behind it to see if there is any housewrap.