Were they stickered in such a way as to allow uniform air flow? Also, was there a time of day where they were in direct sunlight?
For future reference never ever leave a glue up partially finished for a few weeks. Wood WILL move. Once you start the process make sure you have enough time to bring it to completion. Even though your wood was dry you introduced a fair amount of moisture into it with the glue.
Usually when I am gluing up a top for a counter or a table what I will do is plane and joint the wood over a period of a couple of days. By that I mean I will flatten one side then plane the other side flat and joint one edge leaving the pieces over thickness and over sized. Then I will stack the pieces with stickers between each layer and leave them over night. Not in any direct sunlight ever. Then start the process over the next day. Taking off just enough to flatten and joint then plane. If I am not going to be able to glue up the top that day I will again leave it over thicknessed and only bring it to final size when I am ready to glue the entire top. Then at glue up I will ensure proper clamping pressure on both faces and that each piece aligns with the next. (within a 64th). I have a 38" drum sander in my shop so I can sand flat tops up to that width. If they are wider I will make the top in two halves and then sand each of them flat before gluing them together then I only have one seam to clean up.
Before I got the sander I used to do my clean ups and flatten the top with a mix of scrapers and sanders using straight edges to ensure I didnt cause any dips etc. In your case if you only have the 12 or 13 inch planer you can do the same as you did if you are going to run them through there but do your final glue up immediately dont leave it sit.
Hope this helps
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