I am running Transmission-daemon and whenever I download something the CPU usage spikes to around 99%. I have to use NTFS because of my many windows machines. I would prefer not to format because I have around 3 TB worth of stuff to store. Is this a common occurrence?
As Jaromanda X said in the comments, a few google searches on NTFS Linux performance shows this is not uncommon.
Probably the first step gleaned from several threads on the topic is to use lsof to verify which process is slamming your NTFS partition: we're assuming Transmission but maybe it's something else:
sudo lsof /path/to/NTFS
One thread suggests that disabling updatedb.mlocate from cron was a big help. Another thread suggest small writes to the Linux NTFS FUSE driver are particularly CPU intensive, and that would be exactly what a BitTorrent client would be doing. One option might be to look into increasing cache sizes in Transmission to have less frequent writes.
Additional reading suggests more fragmentation makes the CPU utilization worse, and certainly a larger filesystem with lots of small writes (ie. BitTorrent) is likely to have high fragmentation.
So the short answer to your question of "is this a common occurrence" is: yes, high CPU is a known problem with NTFS drivers doing writes on Linux. There are any number of things you might be able to do to help tune to make it better, but you've got a lot of trial and error testing ahead of you, there doesn't seem to be any consistent "fix all" answer for the performance issues you are seeing.