Voltage Spikes on Digital Pin

@Delta_G: I try to avoid posting information from various reasons. I am ashamed for low quality code when it is in the "testing" phase. Also I doubt anyone will read 1000+ lines of code including 10 libraries "found somewhere on internet" with cryptic comments everywhere. So I try to remove as much unnecessary code as possible and add comments to make it clear. Similar goes for circuit - if I have a schematics it is hard to understand unless you remember what I meant when I draw it. I need to redraw it cleanly before presentation. And the physical circuit is similar mess, often on more than one breadboard, sometimes with other unrelated projects on other part of the breadboard ;-). There is no chance to track jumper wires from a photo.
Cleaning a project to be "worth presenting" takes a lot of work. While doing so, I often find the bug myself. But it is tempting to ask without showing anything, skipping all the boring work - maybe someone guesses the answer anyway.

@Timbergetter: Please, show what was causing this, I am curious. My guess is a SW bug.