Shaw and Mainoo both started for Man Utd in the 1-1 draw at home to Tottenham at the weekend, but their involvement in the Spanish capital on Tuesday night has since been placed into serious doubt.
As the Man United squad were put through their paces at Carrington on Monday morning, neither player took part in the training session.
Shaw was substituted in stoppage-time against Spurs and later spotted limping as he made his Old Trafford exit, while Mainoo completed the full 90 minutes.
Carrick is due to name the United travelling squad and is expected to provide an update on the pair in the news conference on Monday evening.
If Shaw is forced to miss a second Champions League match in succession, it would leave the Man United head coach with a selection dilemma at left-back as Patrick Dorgu and Noussair Mazraoui are also sidelined.
Therefore, Carrick could move first-choice right-back Diogo Dalot to the opposite flank, thus making minimal changes to the defence that started at the weekend.
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Alternatively there is also the option of moving Lisandro Martinez across or handing a start to Ayden Heaven or fellow youngster Harry Amass.
In midfield, United are well placed to cope if Mainoo has to miss out. Carlos Baleba could make his full debut after a substitute appearance against Spurs and Andrey Santos is pushing for more minutes having not featured in the two games either side of the international break.
Bryan Mbeumo put forward his case to continue up front, in the absence of Benjamin Sesko, with a goal at the weekend but Amad Diallo and Matheus Cunha are at risk of making way for Marcus Rashford and Joshua Zirkzee.
Predicted Manchester United XI: Lammens; Yoro, Maguire, Martinez, Dalot; Tielemans, Baleba; Amad, Fernandes, Cunha; Mbeumo
Injured: Ugarte, Dorgu, Sesko, Mazraoui, Heaton
Doubts: Shaw, Mainoo, De Ligt
How to watch: Amazon Prime
Venue: Metropolitano Stadium