The cracks are probably stress fractures. If the cracking isn’t too bad, you can mix up some very fine sawdust with wood glue and putty them in. If you are finding yourself using a trowel though, I would consider the board lost and move on. If there is just one large crack that runs down the middle, cut the board on both sides of the crack and edge glue it back together. As far as prevention goes, give the pallets some time to acclimate in your shop before surfacing and cutting the pieces. I would also recommend not surfacing the lumber until you are ready to work on the project. If you are not going to work on the piece immediately, or if you are taking an extended break from the project, place the boards in a garbage bag. This will slow down the drying and help prevent warping and shrinkage (thank you stumpynubs for sharing that one). Once the pine has a top coat (stain, paint, poly, etc.) it should be safe from cracking due to shrinkage. I would not use thin pine for high stress projects though.
Hope this helps.
David
-- There is little that is simple when it comes to making a simple box.
