Yes but unlikely. This depends on the implementation. The current implementation is that entering an address will result in creating a normal P2PKH output which Bob could spend from. If there is an implementation that a P2WPKH output is created when an address is entered, then it is possible that Alice would, in effect, lose her coins if she used such an implementation.
What you're saying is equivalent to "in theory there could exist some totally busted software that just make up random crap when alice punched in an address, thereby burning the coins"-- this is true, but it's unrelated to segwit.
The recipients address specifies the scriptPubkey that they must be paid-to in order to be paid. If you don't pay to what they've specified, you haven't paid a party. In the OP's example, Bob would have provided an ordinary address-- the same as he provides today, perhaps-- and the payment would work like normal.
How the txin scripts work and txout scripts work are completely orthogonal. Someone can spend segwit coins and the receiver doesn't care, it doesn't change their operation; beyond the fact that their older client will see the payment as a non-standard transaction so their non-upgraded wallet will not display it until it confirms.
