A lag frame happens when the CPU had so much to do in the previous frame, that it didn't finish all of its calculations. Even if the work needed to complete the calculations from the previous frame is minimal, the game still allocates a full frame to finish it off. This frame is essentially a wasted frame in the context of real-time speedrunning since you spent two frames updating the game state only once.
Common Sources of Lag
The minimap requires a significant amount of processing power to display. As a result of the practice hack removing it, the original version had noticeably less lag in many parts of the game, which was especially apparent in Lower Norfair, for Power Bomb lag in The Worst Room in the Game and Red Kihunter Shaft.
Version 2 added "Artificial Lag", which was a feature that added instructions to compensate for the lack of minimap, in order to make the practice hack have approximately the same lag as the original game.
The vanilla game disables the minimap during boss fights, so there is likely more lag than the original game in these rooms, because of the extra instructions performed per-frame by the hack.