I have a marlin 66 22 caliber rifle. The magazine was fine and now does not slide into the the magazine tube far enough to turn and lock in. What has happened? The magazine does not appear damaged

I think you are asking for an EXPLANATION of why, when you put a bullet in a CHAMBER with your fingers the bolt won't close but when you put the bullet in the magazine, it goes in the chamber and the bolt locks DOWN fine. Is THAT a safety system?

ANSWER: No, it is not a safety system. I am assuming that you are speaking of a standard BOLT ACTION rifle in a centerfire caliber configuration. The extractor, located near the bolt face is why it won't close. When you put the bullet into the chamber and then try to shut the bolt, the extractor has to jump over the rim of the shell casing. When you place the bullet in the magazine and then shut the bolt, the bolt face pushes the bullet up out of the magazine allowing the rim of the case to slide between the bolt face and the extractor claw and feed into the chamber. After firing or if you simply just want to remove the bullet from the chamber, pulling the bolt rearward, the extractor claw hangs onto the rim until the case hits an extractor bar causing the shell to fly out of the rifle.
A good question.
I would suggest a firearms training session. Check with the NRA or a local gun club for help.

Could need a new spring in the magazine tube.
Ebay has complete inner magazine tubes.
search for Marlin Model 60 .22 Inner Magazine Tube

not sure if this link will help you out but have a look..
https://en.wikipedia.org/wiki/Marlin_Model_1894 ..
or this one...
caliber year place of manufacture etc of Marlin 1984 Lever Action rifle...

Savage had a long history or caliber changes with that rifle. Anything from for .303 Savage, .30-30 Winchester, .300 Savage, .25-35 Winchester, .250 Savage (also called the .250-3000 Savage, .22 Hi Power, .22-250 Remington, .243 Winchester, .308 Winchester, .358 Winchester, 7mm-08 Remington, .284 Winchester, .38-55 Winchester, .32-40 Ballard, .375 Winchester

The most common stamp showing c3 was for 22

Hi Gary,here's a link to the Marlins gun book, Blue Book of Gun Values MARLIN FIREARMS COMPANY Rifles Centerfire Lever...