This seems highly improbable, so without a working example, I can't suggest anything.
Obviously, if you use the same (non-local/non-instance) variables in each macro, then they will each mess each other up.
And yes, the action is non-atomic - most every action that takes time in Keyboard Maestro is non-atomic.
This is unlikely to happen. The OCR, like the screen search, is a CPU intensive action - if you want to reduce your CPU usage, don't use the action, or don't use the action continuously - put pauses in your macros if you want to use less CPU.
Yes, this is an error Tesseract reports (more or less all the time), and Keyboard Maestro hides the error from you normally. However, if nothing is returned as matched text, then Keyboard Maestro returns the error response, which includes this message.
Cleaning up the image, in particular thresholding it, seems to improve Tesseract’s accuracy (unfortunately, Keyboard Maestro has no thresholding or other image processing actions, so you'll have to use something else for that).