This is a far from normal occurance. It could be that the follower spring in the magazine had failed. On any rifle, if it is not working properly forcing it is not a good idea. It is telling you somthing so you better listen.
I have 13 rifles build on Mosin Nagant receivers and I am a regular on the two sites dedicated to these rifles. I have never heard of this before on any of them. M39's are excellent rifles. But they are not new and careful examination is necessary on any milsurp you use.
I would not use a wooden dowel to try to force the bullet out of the breech it could swell up itself when it hits the tip of the bullet and may get jammed itself. A cleaning rod may do the trick.
Go to this site:
www.gunboards.com/forums/ Check out the Collectors Forum.
Those people there should be able to point you in the right direction for repairs. It may be possible to repair the stock with some Gorilla glue and a few dowel pins. Some people there have down remarkable repairs to badly damaged stocks. I know of no new stocks for these, but they may be able to help you find a used one if yours cannot be repaired. They should also be able to tell you what to look for as to what could have caused the failure to feed properly in the first place. Very knowledgable groups of serious, but helpful collectors.