This has been asked before with no response. The FRY troops must have gone straight through Croatia while they were at war with them in order to get to Slovenia and I find it a little surprising that there are no reports at least of Croatian attempts to sabotage the Yugoslav forces since unlike the Bosniaks Croatians did not have any quarrel with Slovenians as far as I know. Was there any cooperation between Slovenia and Croatia?
First of all, not all of the troops had to go trough Croatia. Military bases were scattered across the SFRY and many were in Slovenia. In many cases the troops would move out of their Slovenian bases towards their objectives (mostly airports and borders checkpoints).
As for your main question, yes, the Croatians did help out. They blocked army columns on their way to Slovenia. From what I remember, they blocked a border check point near Varaždin and an army base in Zagreb. And I'm talking about civilians here, not some kind of militia. I can't find any decent sources about this right now, but even if I did it would be in Slovenian.
The Croatian government didn't do much to help, but then again they didn't have many options. Later, Slovenia sent weapons to help Croatia in their war, but wasn't directly involved either.