A club doesn't need to have completed the signing of a player in order to register him as their player for the Challenge Cup so they could have registered him when they agreed terms with him (but were still awaiting his Visa) rather than waiting until announcing his signing (when his Visa came through) to do so.

Last season Wigan and Warrington both did this regarding Martin Gleeson and Richard Mathers. They agreed not to cup tie the players in round 4 and then each club registered the respective players before the second deadline despite the transfers not yet being completed as they knew the swap was due to take place. Once the transfers went ahead both were able to use the players in their cup campaigns.

If thats the case then fair enough. didnt realise that you can register a player for cup before the signing is completed and he's registered as your clubs player in league.

although having just read the relevent rule it states that the player has to be correctly registered and eligible to play for the club in their normal league competition. So I dont see how you can register a player for cup when they are still registered for another club in the league competition in the gleason/mathers case.

Wrong, there is only one deadline, the latter one you mentioned
before that if you are eligible to play in the league competition you are eligible to play in the cup (unless cup tied)

They would have been registered for the league prior to the deals being completed as well to allow for it. A player doesn't need to be employed by a club for them to hold his registration (Leeds for example held Iestyn Harris's RL registration during his time in RU) so both clubs would have agreed to allow the other to gain the registration for Mathers/Gleeson. The RL registrations would have been switched with neither playing at all in the intervening period before the transfers were completed.

Bit harsh, especially after the situation with Hull last year. Still, how stupid were they to let this player play ?

Hull FC should have been expelled from the competition. There were plenty of precedents for this within the game.

edit
It is harsh on Halifax but the RFL really does need to pull it's finger out and be proactive rather than simply blame the clubs.

Was only a matter of time!