I got a similar issue after accidentally removing the rightmost column in my board configuration.
I'll try to show before and after using some screenshots to explain...
I had columns set up like this:
... and velocity chart was looking fine for completed sprints:
I removed the 'Done' column. This resulted in the 'Done' issue status becoming unmapped...
... which broke my velocity chart for Sprint 2:
If I look at the Sprint Report for Sprint 2 after this, I see that it is now showing issues under the heading "Issues Removed From Sprint" (rather than as "Completed Issues").
This is because the 'Done' status (which these issues were in when the sprint was completed) is no longer mapped to show on the board.
If you haven't already, it would be worth checking if you have any unmapped statuses like this.
Failing that, this Atlassian Knowledge Base article might help you rule out some other reasons: https://confluence.atlassian.com/jirakb/issues-are-not-appearing-in-boards-779159013.html
Anyway, I hope my answer is helpful.
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