A check of my kit also showed part E2 to be malformed, though as you say it can probably be reshaped into the correct position without too much difficulty!
Haven't checked my 2nd kit yet but part E2 and E3 appear to be identical so with my 1st build omitting these parts I should be OK using both E3 parts on my second build??
Though Airfix do need to be aware to rectify the issue as constantly replacing malformed parts will effect the profitability of the kit and future releases, and not good for public relations as some will view it as a major issue
E1 & E2 (not E3) should be intentical, so using two E1's will do just fine.
I emailed Airfix yesterday and got a response very quickly from their Customer Care team asking me to give the batch/trace number on the little white label on the back of the box, they didn't say if it was a wide spread problem or not.
In the meantime I had a pleasant surprise while watching the RAF100 Flypast - the transport section flew over my house at low level. Once I got over the surprise and shock of the Hercules & Atlas going over - I grabbed the camera and photographed the Globemaster & BAE 146