This only seems to happen on my 0.14.22->0.15.1 upgraded map as I couldn't repro it after I made changes to my substation layouts.
Coverage and removal shown here: http://imgur.com/a/4s6p0
This has a simple workaround by replacing all substations involved. Once that is done, I could not repro the problem. So it seems to be something weird with <0.15 substations on the map.
[0.15.1] Overlaping substation coverage fails on removal
Re: [0.15.1] Overlaping substation coverage fails on removal
Can you upload a copy of the 0.14 save?
If you want to get ahold of me I'm almost always on Discord.
Re: [0.15.1] Overlaping substation coverage fails on removal
Should be fixed for the next version of 0.15 
If you want to get ahold of me I'm almost always on Discord.