The Gunners want the payment as they do not believe the Chile and Armenia international are of equal value, despite Sanchez having just six months remaining on his contract.
Mkhitaryan is also only 33 days younger than Sanchez yet his poor displays for United since joining from Borussia Dortmund mean Arsenal want an additional fee.
The Evening Standard understand this is the only stumbling block in the sensational swap deal, with both players having agreed terms with their prospective new clubs.
Sanchez will be paid an eye-watering £27m-a-year before tax and given a £20m signing on fee, while United will pay up to £10m in agents fees; taking the grand total of the move to £145m, according to The Daily Telegraph.
If Mkhitaryan does not join Arsenal – he has also been linked with a loan return to Dortmund this month – then United will pay £35m to acquire Sanchez.
28-year-old Mkhitaryan, who has been left out of United's matchday squad for seven of the last 12 Premier League matches, will meanwhile become Arsenal's highest paid player on wages of around £175,000-a-week.
Arsene Wenger expects Sanchez's move to be completed in the next 24 hours and reports suggest the Chile international is being lined up to make his United debut against Burnley on Saturday [20 January].
The Arsenal boss however plans to deploy Sanchez against Crystal Palace in their own Premier League game happening at the same time if the move collapses or has not been completed. New signings must be registered by midday on Friday [20 January] to be eligible for the weekend fixtures.
It is not expected that Mkhitaryan's move to Arsenal will be finalised in time for him to face Palace and his debut for his new club could be delayed further as he is cup-tied for the Carabao Cup semi-final second leg against Chelsea next week.
He may then be forced to wait until the trip to the Liberty Stadium to face Swansea City on Tuesday, 30 January before making his Arsenal bow.