not sure if this is it but on my teams if i had only two tightends on the depth chart the computer put in the best replacement when my two guys were either hurt or tired. Centers sometimes have TE like skills and since their weight is only like 16 lbs more they get put in at TE. THat's probably what happened :)
The 2 RB/3 TE set can use up your depth chart very quickly. If you use the "PA TE Drag" play a lot, one of your linemen could be used as an extra tight end and then receive a pass.