Bugs afflict the player's Navi during network duel and generally has a negative effect. When the player's Navi is affected by a bug, their emotion window will flicker.
They can be caused in the following ways:
- A NaviCust part is placed in a way such that it does not follow NaviCust part placement rules.
- A mod card with negative effects is installed (Japanese version only).
- The Navi is hit by a chip or program advance (e.g.
MoonBld, 
ElcPuls3, 
BugBomb, 
DestPuls) that causes a certain bug.
Movement Bug
The Movement Bug causes MegaMan to warp to the edge of his field, whenever he moves regardless of the Bug level.
Navi Cust parts causing this Bug
Custom Bug
The Custom Bug starts after a number of turns, depending on the Bug level, and reduces the amount of available chip slots in the Custom Screen by 1 every time the Custom Screen is opened.
The bug takes effect depending on Bug level:
- Level 1: Fourth turn onward.
- Level 2: Third turn onward.
- Level 3: Second turn onward.
Notes
- Custom Bug will not decrease the available chip slots below 2.
- Charge Cross can stall the chip decrease by 3 turns.
HubBatc can be used to stall out Custom Bug for several additional turns by resetting the custom size to the maximum possible.
Navi Cust parts causing the Bug
Panel Bug
The Panel Bug causes MegaMan to crack the pnael when moving off of it. The panel becomes broken, if it was already cracked
The chances of the panel cracking goes a sfollows:
- Level 1: 2/8 cracking panel.
- Level 2: 3/8 cracking panel.
- Level 3: 4/8 cracking panel.
Navi Cust parts causing the Bug
Encounter Bug
The Encounter Bug causes MegaMan to encounter viruses more frequently regardless of the Bug level.
Navi Cust parts causing the Bug
Result Bug
The Result Bug causes the player to only receive Zenny as a Battle Reward.
Navi Cust parts causing the Bug
Buster Bug
The Buster Bug causes the Buster Shot to occasionally be either a jam or a shot with the damage multiplied by 10 instead. This does not apply to Beast Out.
The chances of jams and missfires depends on the level:
- Level 1: 6/16 (37.5%) Jam and 1/16 (6.25%) 10x Damage.
- Level 2: 10/16 (62.5%) Jam and 2/16 (12.5%) 10x Damage.
- Level 3: 13/16 (81.25%) Jam and 3/16 (18.75%) 10x Damage; the Normal buster is deactivated (0%).
Navi Cust parts causing the Bug
Disabled
The disabled bug causes the bugged support program (i.e. Rush, Beat, or Tango) to have no effect.
Battle HP Bug
The Battle HP Bug causes MegaMan's HP to steadily drain during the battle. Depending on how many bugs you have through the Navi Customizer (up to 3) is which level it starts with.
The Battle HP Bug drain goes as followed:
- Level 1: Drops 1 every 40 frames. Starts with this if have 1 HP Bug.
- Level 2: Drops 1 every 35 frames. Starts with this if have 2 HP Bugs.
- Level 3: Drops 1 every 30 frames. Starts with this if have 3 HP Bugs.
- Level 4: Drops 1 every 25 frames.
- Level 5: Drops 1 every 20 frames.
- Level 6: Drops 1 every 15 frames.
- Level 7: Drops 1 every 10 frames.
Notes
- HP Bug level can be increased by Damage HP Bug or by the special properties of certain attacks, such as Erase Tail Arrow or ElcPuls3.
- Using
BugFix will remove all levels of HP Bug regardless of their source.
Navi Cust parts causing the Bug
Damage HP Bug
The Damage HP Bug increases MegaMan's Battle HP Bug by 1 level when hit by a damaging attack without having SuprArmr (causing him to flinch) or a damaging attack that inflicts Drag, such as or 
ElcPuls2.
Navi Cust parts causing the Bug
Custom HP Bug
The Custom HP Bug causes MegaMan to steadily lose HP in the Custom Screen. No Navi Customizer Part gives this bug and can only be received through other means, such as DestPuls. If BugFix is used, Custom HP Bug will be removed.
Custom Damage Bug
The custom damage bug causes a set amount of damage to be inflicted when entering the custom screen. It can only be caused by use of Patch Cards.
Color Bug
The Color Bug inflicts MegaMan with a Status effect at the start of a round. The Status can either be Confused, Blinded, Invisivle or Invincible for a set amount of time with all of them having a 25% chance to occur.
Notes
- Having 5 Colors on Grid results in a 5 second long Status effect.
- Having 6 Colors on Grid results in a 10 seconds long Status effect.
- Transforming into Tomahawk Cross turn 1 will not remove the Confused and Blinded Status.
Emotion Bug
The Emotion Bug causes Base MegaMan's Emotion Window to cycle between Normal,Tired, Angry and Full Snychro every 60 frames and is only active in Base MegaMan when his Beast Counter is greater than 0.
Navi Cust parts causing the Bug