For insects:
* Insect
* Beetle (if it's a beetle specifically)
* Critter
* Pest
* Creepy crawly
* Bugger (informal)
For errors in software or a system:
* Error
* Fault
* Glitch
* Defect
* Issue
* Problem
* Flaw
For something that bothers or annoys:
* Annoyance
* Nuisance
* Irritation
* Pain
For something that's hidden or difficult to find:
* Secret
* Mystery
* Riddle
* Clue
Choose the synonym that best fits the specific meaning you want to convey.