Metal Shavings in rear end

Hello. Im new to the forums as far as just registering but I've been reading over different things here for along time. I have just recently started fixing up my 1998 honda 300 fourtrax 4x4. I replaced all the seals and bearings on the rear end, put a 2 inch lift on it and 27" tires. I felt that everything went well so I tested it a couple of days ago and had no problems. I went thrue several decent mud holes but nothing serious. After the ride I checked it over and found that the left side axle nuts near the final drive were both loose. I went and checked the rear diff fluid and found that it was bad murky brown so I must have not placed a seal right or something i guess. I stuck my finger down in there and found metal shavings. I will tear it down tom morning and see how much damage ive done. Could the axle nuts being loose cause the shavings? Any help would be great. Thanks