Any quick survey of the number of maps of the Israelite Exodus from Egypt will show there is very little agreement on which route was taken - we do not know even where the crossing of the "Red Sea" occurred.
This is all due to our lack of definite knowledge about ancient geography.
The OP's perplexity is due entirely to the unfounded assumption that these places in Num 33:31 and Deut 10:6 were visited only once. Some places, during the 38 years wandering could have been visited more than once and in different sequences.
Indeed, Ellicott specifically quotes a Jewish rabbinical scholar who proposes exactly this idea that very simply explains the apparent discrepancy in the Torah record. That is, that Israel visited some places several times as they traversed the desert. See https://biblehub.com/commentaries/deuteronomy/10-6.htm
Given the length of time the Israelites remained in the desert and the sheer number of times they moved, it would be very surprising if some places were not visited more than once.