I think the notification scheme is probably working fine, but you've not made the changes you think you need to the one that is causing you problems.
First pick an email you didn't want to get. Look at the project that is named in the email, in the issue key. Now look at the project's notification scheme.
Each line in a notification scheme is a rule.
When <event happens>, send email to <various ways to define a list of people>
Most of the events are fixed - issue edit, issue create, work logged, etc. You need to work through the rules in there and decide whether email should be sent for each event.
Personally, I generally start with a rule that is "reporter, assignee and watchers" and then think carefully about if each of them really need it
Edit for example - do you really care if someone edits an issue you reported? Same for watchers. The edit will be caught in the history. As the assignee, you probably do care that someone has edited something you're actively responsible for though.
Log work? Nah, no-one needs that. Except maybe a project lead if they're looking at timesheets and activity.
Avoid the use of groups like the plague, if you want to send to multiple users, use a role instead and put the right users/groups for that project into the role.
Then there is the odd one. Transitions can fire different events. Have a run through your workflow and decide what transitions should email people. Assign appropriate events to each transition that should email people (feel free to create your own custom events, that's what they are for!), and then use those events appropriately in the notification scheme.
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