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Describe the Bug:
AI has Aquus Steed which with 8 0/+1 counters is now 1/11 I cast Transmutation on it and correctly becomes 11/1 then I cast Auger Spree on it and instead of dying as it should become 15/-3 it becomes 7/5.

Which card did behave improperly ?
Auger Spree ? Transmutation ?

Which update are you using?(date,name)Which type(Duel,Gauntlet,Sealed Deck)
Previous update: Manalink update 14 November 2014: Khans of Tarkir + more

What exactly should be the correct behavior/interaction ?
Auger Spree or/and Transmutation

Are any other cards possibly affected by this bug ?
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Actually, that is correct. An example from the comprehensive rules:

Example: A 1/3 creature is given +0/+1 by an effect. Then another effect switches the creature’s power and toughness. Its new power and toughness is 4/1. A new effect gives the creature +5/+0. Its “unswitched” power and toughness would be 6/4, so its actual power and toughness is 4/6.

To be specific about your case, the creature has a natural p/t of 1/3. There are no layer 7a or 7b effects. Layer 7c is p/t modifiers so the +4/-4 is applied making it 5/-1. Then layer 7d applies the counters making it 5/7, then layer 7e switches p/t, resulting in 7/5. State based actions are then checked and all is good.