I read up about this when I had the same concerns with mine.......apparently it is often a simple case of the eggs being laid with a protective coating, and the latter ones laid, (sometimes all) arent coated as well, so they absorb more water, which is stained by the vermiculite, resulting in a brown egg. If it was laid in the water then maybe some of that coating was washed off?
I also read that the embryo doesnt attach in the egg for several hours after being laid, and so even if it was in the water, as long as you caught it in time it will have settled with the air bubble at the top and the embro will be just fine 
I dont know how much truth is in this, I found it on a page re bearded dragons a week or so ago, but it really put my mind at rest after one of Elvis's eggs literally bounced off a rock 
I candled it yesterday and it has some nice fat veins inside so I assume it is ok. As for the sand, I wouldnt remove it, incase it is firmly fixed and damages the egg
-----
Kel
www.collaredlizards.co.uk
0:0:1 Timor Monitor
2:3:0 Collared Lizards
0:0:2 Chinese Water Dragons
0:0:1 Dune Scorpion
0:0:1 Imperial Scorpion
1:0:0 Desert Hairy Scorpion
0:0:1 Mexican Red Knee Tarantula
0:0:1 Green Tree Frog
0:0:1 Grey Tree Frog