MTGArena aggressively manipulates what kind of deck you will play against (which disables the ability to make a counter META deck, since after picking a few counter mechanisms you're very rarely going to be put against the archetype you foil even if you hunt half the field), manipulates who goes first (some Streamers stand at recording over a thousand games and have gone first under 30% of the time, current formats are extremely powered up so the first turn advantage is the deciding factor of who wins often), and manipulates opening hands (something the devs have blogged about).
While harder to prove MTGArena also buries/floats cards. Some cards have patterns of existing in your opening hand or only after your 17th-22th draw, others occur in your opening hand more than 50% of the time, some truly toxic cards like Agent of Treachery are likely to have 3 of 4 of your copies in the last 20 cards. (Agent of Treachery is the easiest to see since such decks also have to tools to cycle through their deck and stall out the game to see their whole deck).
The shuffler also has a habit of giving duplicates of cards or making someone draw a duplicate of a card more often than "expected".