Not sure if this has been brought up but on two of my teams in preseason i had two kickers on my depth chart and instead of subbing in the second kicker it put wr's and linebackers at kicker for 3 quarters of the game.
This thread is correct, what is happening is that the #1 K is getting benched and the #1 P is getting benched because both have a #2 in the depth chart. But since the #2 K is also the #1 P and vice versa, the net result is that you now no longer have an active kicker or punter.
The logic problem is that when you rest your starters, the #1 kicker and the #1 FG kicker are both benched, which removes them from your depth chart. I have this on the slate to be fixed in 0.4.2 hopefully.