The flat slab engine cover / air filter housing on the 1.3 multijet is poor in that it's easy to assemble it incorrectly which distorts the mouldings. If you take off the removable cover via the three bolts and look along the length of the long mating surfaces they're quite often not straight . This happens because the centre one of the three male tongues often doesn't engage properly with the corresponding female portion on the main body of the housing and pushes the back of the housing towards the back of the car bowing it. Engine heat and sun on the bonnet then raises the temperature of the plastic , re-memorising the glass reinforced plastic to a new distorted shape. You need to memorize it back to when it was first moulded . You remove whole housing from top of engine and with a heat gun, gas ring , or blow lamp, carefully heat up the distorted areas and reshape . Take your time and make sure heat is evenly dispersed over a big part of the moulding. Do it slowly and with oven gloves on you can make bent parts straight again. Look along the mouldings's easy to see if they're straight or not. When they are just hold them in position until they cool down or get someone to dribble water or blow cool air on them.
When you've done that it's imperative you install the filter with the whole housing off the car . That way you can see that all three male tongues on the air filter cover are properly engaging with their female sockets in the main housing. You also need to make sure the three cover bolts threads aren't stripped and are tightening down properly . If they're stripped you can use a SLIGHTLY fatter (but a bit shorter ) wood screw to replace any stripped ones. Don't use a crazy fat one or you'll burst the the plastic moulding surrounding the screw .
There's been some talk on here of water entering the engine via the air filter. I think that is more likely to happen when these mouldings are distorted and particularly when the screw threads are stripped because that allows water direct ingress past the front gasket lip into the air aperture on the engine side of the filter . I also think that jet washing the engine bay on vehicles with this type of air filter housing is asking for trouble.