My "nit-picks" are as numerically proceeds:
1) After Bob has been swept off his feet (literally) by the tank with Enzo Matrix behind the controls, Bob reaches for and grasps a hand grenade from his vest. However, the grenade is clearly seen back on the vest when Bob is alarmed to discover Enzo Matrix to be the tank's operator.
2) From where did those hover-boards come after Bob and Enzo Matrix are released from the game and consequently heading to Dot's Diner?
3) As Bob and Dot Matrix stop at the entrance to the stage on which Dot Matrix intends to emancipate Binomes from Megabyte's domination, there is conspicuously some graffiti on the wall to the left of Bob. However, the graffiti was never there prior to and proceeding this close-up shot of Bob.

Don't they carry the hoverboards wherever they go? I thought they folded up very small and were attached to their belts...

"Take out what you put in." They must've rode the hoverboards into the game cube as it dropped.

"Sir" and "Binky" make their first appearances as the bomber crew.

Dot is acting as a representative of the Principal Office and Phong, the recognized authority in Mainframe.
Her character is growing in importance. More than just a leading citizen of Mainframe, she is becoming a LEADER of Mainframe. From here on she is privy to Mainframe's most sensetive places, such as the core control room and the archive. She quickly gets into the habit of taking command in a crisis throughout season 2, issuing orders and coordinating strategy.