Having many small bugs and issues can be an advantage for the following reasons:
- easier to code
- easier to delegate (between developers)
- easier to outsource
- easier to test
- easier to roll back
- easier to merge into upstream or legacy branches
- easier to deploy
It is better to put them in a special JIRA project(s) which can be focused on quality or non-functional requirements.
Of course, this needs to be rational and kept in context. You should only create a couple of each instance/pattern, particularly when they are not being fixed. In such cases, create a 'holding ticket' that will store references to all the individual issues, which is good for systemic vulnerabilities.
You should also aggregate issues in Stories.