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Yes, this is intentional. If you go into endless multiple times, the waves keep resetting after beating the boss, but the ACs keep increasing. This will probably be more evident when there are more bosses added. 

Hmm, I'm having trouble duplicating this bug. If you'd like, you can email over some more specific info at dev@pixelflightgames.com to log the bug report. I know you said you're playing in browser mode, but are you playing on a phone or pc? When the screen went black could you still hear sounds/music? There is an autosave function, if you reload and hit continue run, did it take you back one wave to the boss fight, or did it load the next stage correctly? If you'd like to email this info and anything else you think could help, I'll take a closer look! I'm glad you're enjoying it, and thanks for helping to make the game better!

Thanks for your interest and input! The wizard is intended to be a low health but high damage character, so the initial idea on his ability currently is casting a fireball that can destroy a piece on the board. 

Wow thank you so much for the kind words!