The game contains leftovers from Mega Man 9, such as the stage select mugshots and images from some scenes, as well as Mega Man's unused sliding sprite taken directly from the third game and onwards.
The Bunby Catcher enemy from Mega Man 9. Interestingly, two frames were added, it has the same purple color of Treble, and the sprites are located near a set of Treble's sprites, so it's possible this was intended to take Bass out of pits like the Treble Rescue and Beat Call, the new sprites being for when it was close to releasing Bass.
The charge shot from Mega Man 5 is found amongst the graphics of generic bullets and special effects. In the final game, only Proto Man has a chargeable shot, and he uses the graphics from Mega Man 4. However, one of the prototype builds shows that the Mega Man 5-style charge shot was intended for Proto Man as part of the Sync Up mechanic. Part of a scrapped co-op mode, the Sync-Up mechanic would have upgraded the currently active weapon, and the Mega Man 5-style charge shot was the upgraded version of Proto Man's usual Mega Man 4-style charge shot.
During the cutscene where Treble cures Bass of the Roboenza virus, the latter mistakenly refers to Dr. Wily as an "old cook", rather than an "old kook". This is one of the very few errors that were left uncorrected in Mega Man Legacy Collection 2.
The opening is now displayed after the title screen, rather than as soon as the game is booted.
The Inti Creates logo is no longer displayed, though they are still credited during the staff roll.
Anything that was originally paid DLC can now be accessed by completing the game or entering a cheat code (↑, ↓, ←, →, ←, →, ↓, ↑, ↑, ↓) on the title screen.
Via the "Extra Challenges" mode, Proto Man and Bass are now able to battle against the DLC bosses, Enker, Punk, and Ballade, which was not possible in the original game. However, their weapons still cannot be used by anyone other than Mega Man, nor are Proto Man and Bass able to access the full stages.
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