Hi Terrimorgan,
Based on my test, the logo display well on my side. So, in order to narrow down this issue, I would like to confirm some information with you first:
1. What is the size of the logo icon? I suggest you change the icon to the different size and check it again.
2. When this issue occurred? Was the logo display correctly in team site before?
3. Could you provide the screenshots for us?
Thanks,
Eben Liu