If you have depth chart settings where, say, #1 RG is #2 LG and #1 RT is #3 LG and #1 LT is #4 LG, and you have starters resting, the entire depth chart for LG gets benched and then it is up to the AI to fill it. The AI will try to put in proper players, but once it runs of of non-benched players it just tries to find anyone who can fill the spot. The most obvious situation is where you might have the #1 Kickoffs be the #2 FG and vice versa, they both get benched and because of the circular reference there neither are available for kickoffs and field goals.
I need to add some sort of a warning to validate that this is not going to happen, or maybe even disable resting starters if there is this circular depth chart setting, but right now that is the reason it is happening.