i think this is the first issue you've raised with a challenge system that could genuinely pose a threat to its effectiveness.A lot can happen in 30 seconds in a football match (the limit bandied round on here). There might be multiple things to challenge (example New V Ars there were 3 contentious decisions 2 of which were unable to be determined). Is each individual challenge 1 challenge or can you challenge as much as you like with your one challenge?
but i think it still comes down to the manager/captain or whoever using their challenges wisely and accurately, if you want to challenge 2 separate things in one play then you can, as long as you havent burned through them previously.