Best not to simply just shut the door when feeding - I'd recommend she leaves the crate door open as often as possible during the day so the puppy can go in and out as it pleases. Feeding him in there will help as will giving him chews and/or treats that take a while to get through 
Hopefully with patience it will work - just don't try to force the situation otherwise the pup will be distressed at the very sight of the crate and never be likely to settle in it willingly.
My middle dog HATES crates and would have her muzzle rubbed raw if confined to one yet happily accepts the car cage
Consequently she's never crated and when recently kept in at the emergency vets was kept in a large pen to prevent her becoming agitated (and winding up the other temporary residents!) I bred her and she was used to a crate from the word go as well as carefully and gently being introduced to the concept but she's always had an issue with them so I just don't try and force her. After all, many family dogs for decades (OK, centuries!) have been happily and safely raised without them so it's not really a "must have" item although quite naturally very convenient for limiting access to household dangers when unsupervised (wires etc).
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