I've discovered a bug that only appears with 'Squeak Through' is active.
Basically when blueprinting it will occasionally not mark a tree (maybe other things?) for deconstruction when using shift+click blueprinting. Not sure which ones are the issue or why, but I suspect it's just the dead/burned out ones that might be the issue? Nope live ones are there as well. Going to post this in the forum thread as well.
http://imgur.com/2IMQkdS.jpg
http://imgur.com/jlnSIZ3.jpg
Album = http://imgur.com/a/kMCqq
Running Factorio 0.15.12 and Squeak Through v1.1.7