Level-up crates (as shown below) have been confirmed to grant to bases correctly, however, the game must be restarted for the amount to appear—we have confirmed in all cases that the resource totals at the top of the screen will not update/animate upon leveling up, so please keep an eye on your resource totals before and after restarting the game to see the updated resource totals.
Please see the video below of how this appears upon leveling up and logging back in:
*Please note the resource discrepancy is due to two levels being gained, which is why almost twice the amount of resources appear upon logging back in.