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The foal inherited a Cr from each parent.

Each parent has one CR and one PRL - doesn't matter which parent they got the gene from. So they can throw either the CR or the PRL... so with two CR/PRL parents you have a 25% chance of CR/CR, 25% chance of PRL/PRL and 50% chance of CR/PRL (or PRL/CR, though in reality there is no functional difference between CR/PRL and PRL/CR).

Your foal just ended up being CR/CR - one CR from each parent.

Here is a Wiki article to help explain it https://wiki.huntandjump.com/books/genetics-101/page/what-are-punnett-squares-genes-alleles-loci

No. The heterozygous state (the two genes are different) can never breed true. Only the homozygous state (both genes are the same) can breed true. For example, a Prl/Prl only has Prl as an option to pass down, so the foal will always inherit one of those Prls. But a Cr/Prl has two possibilities to pass down, either the Cr or the Prl. This is true for both parents, so a Cr/Prl bred to a Cr/Prl could produce a Cr/Cr foal, a Cr/Prl foal, a Prl/Cr foal (which looks the same as the Cr/Prl), or a Prl/Prl foal.

Yes, it can be. :P That's why I moved away from breeding phenotypes that need to be heterozygous for lots of things. I loved my blanket appy chocolate palomino duns with ND1, but it was just too hit and miss.

Another option is to breed a line of Cr/Cr horses and a line of Prl/Prl horses and cross them when you want to be sure to get all Cr/Prl offspring.

so you would get 25% Prl/Prl 25% CR/CR and 50% Prl /CR or Cr/ Prl ( basically the same the phenotypically )

It doesn't matter if they are Cr/Prl or Prl/Cr. The inheritance will be the same. You can always GMT the foals for 1 gmt each if they are the wrong gene.