The duo was at fault in United's 2-0 defeat against Tottenham at Wembley where Phil Jones scored an own goal and similar was the case when United made a trip to St. James' Park to face Newcastle United.
Manchester United have only conceded 19 goals in the Premier League this season, the fewest of any team.
Both Jones and Smalling were involved in the defeat and were heavily criticised for their performances as frustrations continue to grow.
United have been linked with a £50m summer swoop for Leicester City defender Harry Maguire, while they could take advantage of the growing turmoil at Real Madrid with a move for France centre-half, Raphael Varane. "Against Newcastle did they make many mistakes, no, but they created a nervousness and a tension".More news: The Queen Helps Environment By Banning Single Use Plastic On Royal Estates
"They were making decision that were unusual".
"They were making decisions all day where you were thinking: 'What are you doing?' They brought these two as the best young centre-backs in England".
The 28-year-old was then booked for diving which led to Newcastle's winning goal in the second half, with Matt Ritchie scoring from the resulting free-kick.
Having already bought Eric Bailly and Victor Lindelof in his first and second summer in charge, two big names are set to be shipped out.
Virgil van Dijk joined Liverpool for a world record £75m [BBC Sport] and Aymeric Laporte swapped Athletic Bilbao for Manchester City for £57m [Sky Sports] last month, and Mourinho wants United to mirror that investment according to the report. The former, however, picked up a niggle during an global duty and required an ankle surgery for it.