The ref deemed a challenge by Danny Shittu on Hanley as a trip and pointed to the spot.
Millwall players were incensed by the decision, especially Shittu who protested that he did not make contact with the player.
Jordan Rhodes buried the spot kick to move Rovers five points clear of the drop zone, but Lions manager Kenny Jackett was convinced that it was a dive by Hanley.
When asked for his view on the incident Bowyer said: "I don't think we should be talking about that.
"We should be talking about our second-half performance and how brave my players were. Some you get, some you don't.
"I thought it was a great run from Hanley, he deserves credit for that, and from where I stood I jumped up because I thought it was a penalty."