well, that's true, it's due to weld tool , you wanted to weld those vertcices , and that's what you get, because of the angle btw the edges in the midle : the big it is the more you get that burned effect. the small is that angle the less that effect appear.
when you detach them the angle btw them is canceled and reconized as 0 so you get a good effect a clean one.
" you can see that in real life too, if you use a plastic and try to break it using your hand , there is a similar effect in the midle, i mean in the place where the forces is focused, but if you use a knife and cut it the plastic, it will looks clean like if nothing was done on it
here i've created a quic shape close to the one you have just to show you how to fix that :
hope this will help
you can check the tutorial : how to chamfer , it's an other way to fix that small problem
if you have any question about any step, please let me know, and i'll explain it .