i noticed this kind of behavior myself right from the off, but I know exactly what you mean they do choose the werdest paths.

I noticed it when on one map a few were just disapearing off the map after ships under attack warning, i was baffled so i went back and watched em, they were back tracking through explored space and ging straight through a gravity well that was known to be a pirate base.

In short yeah they've always been a bit dumb in this regard lol It does make sense though because all ships, once assigned either user defined or automatic destination, are programmed to find the quickest route to their destination.

not one i know of,,,who knows it might have been one of those scouts you built earlier passing through ive done that a few times

They've always been whacked like that.  One of the AI's that needs a dramatic improvement.  Is it so hard to ask for it to not backtrack more than one jump, and not run through a pirate base (occasionally pirate bases have more than one warp line, and scouts love to just take a short-cut across them...)

I usually build 5 and turn 'em loose.  generally I have 3 left by mid-late game.  this is inefficient, but it lets me work on other things.  and when I get the opportunity, I manually explore.