You're correct; it will have space on the next hardware reset.
This happens because somebody's getting a mission to DDoS this server. After a DDoS, hardware is damaged, reducing the total space. Then, when the software regenerates, it goes on the hard drive despite exceeding the space limit, resulting in the 246 / 100 you're seeing.
For NPCs, hardware (including hard drive space) will automatically regenerate once an hour, shown in the right pane under the buttons. (In your screenshot, it'll regenerate 48 minutes later.)
As soon as it regenerates, you need to upload your file. Make sure you actually complete the file upload, since if you only have it queued, when you try to complete it, the operation will fail. (I believe this happens even if you try to resolve a queued upload after a hardware reset -- the uploaded file ID will not exist.)