Dozens of issues have been entered into my project on github that have no place there. Some Einstein ran a script and created all these nonsensical issues through the api. Nothing is linked to these issues.
Surely there is someway I can delete them, but I can't seem to find it in the docs.
There is no way to actually delete the issues. What you can do, to indicate that this was a spam attack, is create a new label. You can then use the API to edit each issue to be closed and labeled with the SPAM label. Those who look at it will see the label displayed along side the issue and it's really the best you can hope for.
If you're more comfortable with a specific language, check for a library written in it to make your life easier too.