The tactic you are speaking of is referred to as 'hiding gems' It is frowned upon by many players but still used by a lot of experienced guilds.
The tactic is to deliberately lose gems during the battle and not retrieve them until the end to surprise the other guild.
Often if a guild is winning by a lot they let their guard down and decide that they do not need to put up much of a fight.
Although it is kinda 'dirty', there is no reason why they should not be able to lose and retrieve their gems strategically.
It is hard to counter this type of play so I don't have any tips for you but hopefully knowing what it is will help you prepare for it and maybe even use it to your advantage.
In my guild when we are way ahead, I always check the other team. If I see that they lost a lot, I keep that in mind, because in theory you have to add those negatives to their Delta in order to not get surprised in the end. Also trap level tells a lot about their skills. For example account levels 45+ but still low level traps (Tier 1&2) or almost all low level account (< 26), which can't find Golden gems. Guilds that look like that are nowhere near to be a threat.
As Chaos already said, at the end of a GvG make sure to win with just a little (better safe then sorry, don't let them surprise you in the last minute). The higher your Delta at the end of GvG, the harder next fight will be...........most likely.