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I recently accidentally created millions of files in one folder (rougly 5 million) and due to limitations I couldn't process them correctly (maximum argument count exceeded for wc / ls and such stuff). So I deleted them, which took quite a while, but now they're gone. I deleted the files with a regular rm. It weren't any system files.

So the files are definitively deleted, but the system is very slow on file stuff now. ls, cat and auto-complete by pressing tab freezes the terminal for several seconds.

Is this some sort of fragmentation issue? Is it an issue with the files beeing still somehow present?

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it's not fragmentation issue since ext4 file system can't be fragmented. Install BleachBit and try to clear unnessesery files and cache which can cause your problems. –  Alen Sep 14 '12 at 21:43
Yes it can @Alen , it can be fragmented, but it's not as alarming as NTFS. –  Uri Herrera Sep 14 '12 at 21:44
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