Ahoy
@JRamPirate13,
I'll answer your questions in order:
1. Am I the only one that notices that enemy ships sail in circles?
A: Yes, AI ships are programmed to run circles around player ships when engaged in combat. It isn't a bug, and it takes a bit of finesse and muscle memory to get your broadsides correctly everytime, and there are times where your broadsides will go in directions out of your control.
2. Also, why do Jolly ships attack you when you're in range of them, but Navy/EITC ships don"t unless you attack first?
A: Jolly Roger's Ships, along with the Spanish/French Undead are attack on sight, and are what are considered to be the endgame class of ships used by the main antagonist, who is spoken by lore to rid the sea of pirates who do the bidding of Sparrow.
On the other hand, Navy and EITC vessels are based on a notoriety system out at sea, which can be found over the hull integrity of your ship (Top Left). Once you've attacked a vessel that is acquainted with the Royal Navy/EITC, you will have a mark over your head, which will level up to
Three additional times until you've reached Rank 5, which brings the largest and most powerful ships in the Royal Navy after you.
EDIT: Example of the Notoriety system icon shown here: