Yes, this is something to be expected from printing on PVC.
As you may or may not be aware, PVC is a notoriously difficult substrate to print on, and brightness, contrast, and clarity can differ due to slight variations in the sheets used, the clarity of the ink used, and uncontrollable environmental conditions, such as humidity during the manufacturing and transportation of the PVC sheets between factories. Because of this, no two print runs are exactly alike.
While we are continually looking for ways to increase the quality in printing, we have done the best that we can given current printing technology available. This is the tradeoff necessary to produce cards and sheets that should last for years and never require replacements or sleeving.
We have determined that this should not impact gameplay in any meaningful way. While you may be able to tell which set the Loot or Trove Loot is coming from, you should not be able to tell which card it is, specifically.
There should have been a cover card included with both the decks for Undertow and for Too Many Bones. The cover card is intended to be used to mask encounters before they are drawn. If you are mixing both games together and find the color variation with the Loot decks to be too distracting, we would recommend using the other cover card for your Loot deck, and keep your Trove Loot in the "chest" tuck box.
If you are having a lot of difficulty reading specific cards due to contrast, they may require a replacement. Please submit a support ticket HERE, and we would be happy to help you!