I play a similar wide 4-2-3-1 usually, and in fact use a BWM and RPM-S.
I think your problem might be your flanks. Both your IFs are set to attack. I dunno Thorgan's work rate off top of my head but I'm guessing it isn't super high, and Commons is what, like 32? Either way those guys probably aren't helping your wingbacks much.
I'd also change them from wingbacks to FB-automatic. If you are in attack mentality they'll be playing basically as wingbacks, in control, they will be supporting fullbacks. With your AMC set to attack, he is also bombing into the box. This is too much attack with the 2 inside forwards making runs between the fullback/center back channels. He needs to be a pivot at the top and sliding balls to him (AP support). Setting the AMC to attack is better if you have winger slinging in crosses.
Speaking of which, you probably should. Your IFs would be better off inverted (right footed on the left, left on the right). And Commons would probably be better off as a support winger for sure.
The quickest fixes would most likely be to set Disciplined and Play Narrow instructions. This will keep your attacking mids from going walkabout when defensive duties come in. It will also close the gaps between your defenders so they don't get run between too much. Then I'd tweak your attacking mids a bit. Try swapping sides and changing them from IF-A to W-S. Or a combo. If they are both wingers flinging balls into the box keep your AMC to attack or even Treq. or Shadow Striker so he'll run onto the end of some of those crosses.
I don't know Armstrong and Miller very well but if you want to go with this more crossing tactic check their reactions, jumping, heading ability, etc, and choose floated/whipped/low crosses according to what suits them best.
Hope this helps a little! Good luck!