A kicked ball hits the ground before a fair-catch signal is made. After the ball hits the ground the return man signals for teammates to stay away (hands waving below waist), is it legal for him to pick up and return the ball. (College rules) Also, once the ball hits the ground are the fair catch related rules not applicable?
This is not necessarily 100% clear in the rulebook, but it does seem that "in the know" folks think this is clear (albeit with the grain of salt that refs don't always enforce this consistently).
From the NCAA rulebook, Rule 6 (Kicks), Section 5 (Fair Catch):
ARTICLE 2. No Team B player shall carry a caught or recovered ball more than two steps in any direction after any Team B player gives a valid or invalid fair catch signal (A.R. 6-5-2-I-III).
Invalid fair catch signal is clarified up in Rule 2 (Definitions), Section 8 (Fair Catch):
ARTICLE 3. An invalid signal is any waving signal by a player of Team B:
a. That does not meet the requirements of Article 2 (above); or
b. That is given after a scrimmage kick is caught beyond the neutral zone, strikes the ground or touches another player beyond the neutral zone (A.R. 6-5-3-III-V); or
c. That is given after a free kick is caught, strikes the ground or touches another player. [Exception: Rule 6-4-1-f]
So the primary question is, "Does waving the arms below the belt qualify as a "waving signal"?" The timing is irrelevant (as b. clarifies, invalid signals can be made after the ball hits the ground or are caught, and are still considered invalid signals).
This detail isn't clarified in the rulebook, but it seems a reasonable interpretation that waving other players off is a "waving signal", and in fact may well have been specifically considered by the rules committee given that terminology. As such, it is a reasonable interpretation that this would be considered an "invalid fair catch signal", which means the ball cannot be returned.
This question is likely referring to this game between Northwestern and Wisconsin on 11/21/2015.
Mike Pereira (a former NFL VP of officiating) notes on twitter, for example:
Those asking about the invalid fair catch signal Wisconsin, that is a correct call. The get-away signal is invalid by rule.
Absent a specific instruction in the referee's handbook, it's unlikely to be clarified further than that (unless the Big Ten chooses to clarify it further themselves, which they may or may not).