Bugs afflict the player's Navi and generally cause negative effects. When the player's Navi is affected by a bug, their emotion window will flicker. Bugged NaviCust parts usually retain their function, but cause extra effects on the player. The only exception to this is the Deactivated Bug. All bugs can be fixed by using the 
BugFix chip.
The NaviCust part BugStop will prevent any bug caused by the NaviCust from occuring, as long as it is on the Command Line.
Bugs 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 Patch Card with negative effects is installed (Japanese version only).
- The Navi is hit by an attack that causes a bug. Examples include, (e.g.
MoonBld, 
ElcPuls3, 
BugBomb and 
DestPuls)
Movement Bug
When moving, Movement Bug causes MegaMan to warp to the corner of the field in the direction of the movement. Movement Bug only has one level.
NaviCust parts causing this Bug
Patch Cards causing this bug:
Custom Bug
When active, Custom Bug causes the player to lose access to one chip slot every turn. The effect starts after a number of turns, depending on the level of Custom Bug. Custom Bug will not decrease the available chip slot below two.
The bug takes effect on:
- Level 1: Fourth turn onward.
- Level 2: Third turn onward.
- Level 3: Second turn onward.
Notes
- Charge Cross's passive effect can stop the custom space from decreasing for a maximum of 3 turns.
- Using
HubBatc sets custom size to eight, afterwhich it will continue decreasing by one each turn.
Navi Cust parts causing the Bug
Panel Bug
Panel Bug causes MegaMan to have a chance to crack any panel they move off. If it was already cracked, the panel becomes broken. The chance of cracking the panel increases depending on the bug level, up to level 3.
The chances of the panel cracking goes a sfollows:
- Level 1: 2/8 (25%) cracking panel.
- Level 2: 3/8 (37.5%) cracking panel.
- Level 3: 4/8 (50%) cracking panel.
Navi Cust parts causing the Bug
Encounter Bug
Encounter Bug has no impact on PvP matches. It causes MegaMan to encounter viruses more frequently regardless of the Bug level.
Navi Cust parts causing the Bug
Result Bug
Result Bug has no impact on PvP matches. causes the player to only receive Zenny as a Battle Reward.
Navi Cust parts causing the Bug
Buster Bug
Buster Bug causes Buster Shots to randomly be either a misfire, or a shot with the damage multiplied by 10. This does not apply to Beast Out's Beast Buster. The chance of a misfire, and a powered up shot increases with bug level.
The chances of jams and missfires depends on the level:
- Level 1: 6/16 (37.5%) Jam, 1/16 (6.25%) 10x Damage and a 9/16 (56.25%) normal buster.
- Level 2: 10/16 (62.5%) Jam, 2/16 (12.5%) 10x Damage and a 4/16 (25%) normal buster.
- Level 3: 13/16 (81.25%) Jam, 3/16 (18.75%) 10x Damage; the Normal buster is deactivated (0%).
Navi Cust parts causing the Bug
Deactivated
The Deactivated bug is unique in that the bugged programs lose their functionality, but do not cause any other negative effect. This still causes the emotion window to flicker, and counts as a bug for the purposes of the chip 
Static. Another unique behaviour caused by this, is that this bug will cause the affected NaviCust part to not work even when added by a Patch Card. Attempting to remove this bug by using the chip BugFix will not work, and the bugged NaviCust part will not function.
Battle HP Bug
Battle HP Bug causes MegaMan's HP to steadily drain during the battle.The maximum level of Battle HP Bug caused by the Navi Customizer is 3. This can be increased by Damage HP Bug, or other attacks that increase HP Bug, such as Erase Tail Arrow or ElcPuls3.
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
- Using BugFix will remove all levels of HP Bug regardless of their source.
Navi Cust parts causing the Bug
Damage HP Bug
Damage HP Bug increases MegaMan's Battle HP Bug by 1 level when hit by a damaging attack that flinches, or causes Drag.
Navi Cust parts causing the Bug
Custom HP Bug
Custom HP Bug causes MegaMan to steadily lose HP while in the Custom Screen. No Navi Customizer Part gives this bug and can only be caused through other means, such as the Program Advance DestPuls, or Patch Cards.
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 the use of Patch Cards.
Color Bug
Color Bug causes MegaMan to start the battle with one of four Status effects. There is an equal chance for any of them to occur (25%). Level 1 causes the status to last for 300 frames (5 seconds), while level 2 lasts 600 frames (10 seconds). Using BugFix will not remove any of the statuses applied by this bug. If MegaMan changes into a Cross or Beast out, they will not recieve the Invincible status for that round.
These statuses are
Notes
- Transforming into Tomahawk Cross turn 1 will not remove the Confused and Blinded Status.
This bug is caused by:
- Level 1: Having 5 different colors in the Navi Cust.
- Level 2: Having 6 different colors in the Navi Cust.
Emotion Bug
Emotion Bug causes MegaMan's Emotion Window to cycle between Normal, Tired, Angry and Full Synchro every 60 frames and is only active in Base MegaMan when his Beast Counter is greater than 0. The chances for each Emotion varies depending on the current emotion MegaMan is in:
| to Normal | to Tired | to Angry | to Full Synchro | |
|---|---|---|---|---|
| from Normal | 14/16 | 1/16 | 1/16 | |
| from Tired | 14/16 | 1/16 | 1/16 | |
| from Angry | 7/16 | 8/16 | 1/16 | |
| from Full Synchro | 7/16 | 8/16 | 1/16 |
Navi Cust parts causing the Bug