Cells highlighted in red indicate a time shortage, that is, a day when you got less time than was scheduled for that day (according to the Scheduled Time versus Actual Time settings).

For example, if you marked a 5-hour block of time in the Scheduled Time area but only put 4.5 hours in the Actual Time area that day, the Hours cell for that day becomes highlighted as an indication that there was less Actual time than Scheduled time.

The box becomes red-shaded regardless of how much or how little time was missed. It's just a way of allowing you to quickly spot days where there was some missed or denied time.