The basic rule for D1 regards tryouts, and I believe that there have been no recent changes to the rules.
The general statement is that A member institution, on its campus or elsewhere, shall not conduct (or have conducted on its behalf) any physical activity (e.g., practice session or test/tryout) at which one or more prospective student-athletes (as defined in Bylaws 13.11.1.1 and 13.11.1.2) reveal, demonstrate or display their athletics abilities in any sport except as provided in Bylaws 13.11.2 and 13.11.3.
Of course there are exceptions, and in this case the exceptions are somewhat conflicting.
The exception that (I suppose) most colleges would use to permit scout games is:
13.11.3.2 Activities Not Involving Institution’s Staff. The use of a member institution’s facilities for physical activities by a group that includes prospective student-athletes shall not be considered a tryout, provided the institution’s athletics department staff members or representatives of its athletics interests are not involved in the conduct, promotion or administration of the activity (other than activities incidental to supervising the use of the facilities) and are subject to all applicable NCAA recruiting legislation (see Bylaw 13.11.1.5). (13.11.1.5 applies to basketball.)
However, there is another exception (13.11.3.5) which specifically addresses High School, Preparatory-School and Two-Year College Practice and Competition. Perhaps either the NCAA or a school's compliance officer may have decided that "activities" don't include practice and competition (reasoning that otherwise 13.11.3.5 wouldn't be necessary). Since scout teams aren't mentioned, then one could conclude (although I wouldn't) that games between scout teams aren't allowed.
There is a proposal to modify 13.11.3.5 that recognizes that the current rule is very difficult to monitor, and/or to demonstrate compliance. The rule currently also doesn't consider the differences between individual and team sports. The proposal is in the early stages of consideration, but would IMO have the effect of liberalizing the existing rule.
My opinion is the blanket rule (13.11) is against (paraphrasing) physical activity at which a prospective student-athletes reveals, demonstrates or displays his athletics abilities. 13.11.3.5 is an exception which allows activities under restrictions which scout teams could comply with. So I think somebody has gotten over-zealous. Perhaps the NCAA has issued some sort of "clarification" or "guidance."
Note that none of these rules affect a player's eligibility-- it wouild be an institutional violation.