There is a disconnect within the Trump campaign on that point. Trump is peddling a political message of "voter disenfranchisement," which is generally taken as absence of caucus or primary. This message is a simple sound-bite message that easily resonates with the public. It's a political message, and a falsehood! But hey, it works. It probably helps his chances, hurts Cruz's chances, and it also undercuts the RNC/GOP. All of those ultimate goals are ones he holds, so he isn't cutting against his various missions.
Manafort, on the other hand, says there is no problem at all with the Colorado system or the Colorado rules. The issue as Manafort presents it is that the rules were not followed. That is a more complex claim, probably has multiple instances of alleged dirty trickery, not all following the same pattern. The reality doesn't fit into a political sound-bite message, but he (Manafort) or a person working under his direction will make the appropriate challenges, which will be dealt with either according to the rules, or according to the desired outcome - just like every other decision made in politics and in law.
I suspect Trump knows what the real issue is, and is deliberately making life difficult for Priebus and the power-brokers in the Colorado GOP. Put 'em on the defensive. Certain individual people will NEVER work in Trump's favor. He knows that, and he has to smoke them out before he isolates them from power, if he can.
Trump is calling “unfair” to the RNC/Gop every day. He is setting up to blame them if he loses, as he will not take responsibility for any loss he suffers.
Here is an example that shows he will never take responsibility for even a small error/mistake/misspeak:
He called the Biblical, 2nd Corinthians, “Two Corinthians”. When that was pointed out to him, he said, “Some foreign countries call it Two Corinthians.” That is psychologically Trump - never, ever, admit a weakness, an error, a mistake, find a way to “fix” it, explain it away, so he is never wrong.