Here is the errata for Savage Worlds Deluxe. There is no mention of changing dice rolls.
In practice, this issue will rarely show up. Consider rolling a d4 or d6 to hit a target number (TN) of 6. The d4 has a slightly better chance of being successful.
d4: 1/4*3/4 = 3/16 or 18.75%
d6: 1/6 = 1/6 or 16.66%
However, skill rolls are only part of the game. Even though increasing fighting from d4 to d6 is slightly worst for a TN of 6, it also provides a +1 parry. There are several edges that require skills of a certain die, forcing you to upgrade them.
Finally, remember that the advantage only holds true for specific TNs. With our d4/d6 example, the d6 is more likely to hit a TN of 8 than the d4 is.
d4: 1/4*1/4 = 1/16 or 6.25%
d6: 1/6*5/6 = 5/36 or 13.88%
And of course, the more sides a die has, the greater the average roll is. As you reach ever increasing TNs (ex: shooting a man with cover from a moving vehicle), higher dice still provide better odds.
Because this problem only applies to very specific TNs (d4/d6 with TN of 6, d6/d8 with TN of 8, etc), I would only compensate for it if your players are trying to abuse it (and the at most 2% advantage they get bugs you). You can easily add 1 to the TN, breaking their strategy without really changing gameplay.
tl;dr The problem you mention is a tiny edge case that has an extremely minimal impact on actual gameplay. A player keeping their skills intentionally low will inevitably regret it as challenges become harder.