The creators of Mega Man 9 are really going all out in trying to make it just like the NES versions.  Glitches such as screen flicker, slowdown and others will happen, just as they would before.  Also, there can be no more than 3 enemies on the screen at a time.  Most of these old-school bugs will adjustable.

“Gamasutra: You talked about how people were trying to graphically exceed the capabilities of the Famicom, but what about the temptation to exceed some other capabilities, such as flicker, slowdown, sprite limits, and stuff like that? Was it really hard to get people to stay within the confines of what they could have done, if this had come out after Mega Man 6 in 1993? 

HT: Yeah, there were some things, like you couldn’t have more than three enemies on the screen at once, so we had to make sure that that’s how it stayed in our game. In the part with the dragon with the flame, [there should be] flickering, and whatnot. 

In the options of this game, you can adjust that, unlike the old games. We purposely put some of those old-school bugs into this game, so it does recreate that feel.”

*Insert screen flicker*

Read the full interview by gamasutra Here