These are only small visual problems, but:
Depending on the manga, the x-axis doesn't start at zero - Example: Isekai Cheat Magician
When there are only a few votes, the x-axis shows decimal places - Example: Sukumi's! (and again, the x-axis doesn't start at 0)
When using two-page rendering with fit display set to "Width" the first 15 pages of this chapter look awful:
I guess that this is caused by the different image dimensions (In the screenshot: 2762x4043 and 1300x1899) of those pages.
The other display-fit options don't have that problem.
The "Last Updated" column on some manga pages is incorrect.
Examples:
http://mangadex.org/?page=search&title=Toujuushi%20Bestialious
http://mangadex.org/?page=search&title=Samurai%20Sensei
Both of them have one chapter, but were apparently never updated.
After uploading them they had a group...
The author-link on the manga page leads to a search for the author,
e.g. https://mangadex.org/?page=search&author=ONE
While the author-link on other pages (e.g. when searching, or simply browsing the manga list) leads to a modified "Titles"-tab,
e.g. https://mangadex.org/?page=titles&author=ONE...
E.g.: https://mangadex.org/quick_search/hero#
The quick search page shows multiple pages with results at the bottom, but the links themselves lead to empty search results:
https://mangadex.org/quick_search/0/2/, and so on