So this one is wierd, but it is definitely caused by some interaction between ThaumicEnergistics and Thaumcraft.

Infusion recipes that have specific shard in them can have those shards substitued for others.

Example:
Sinister Lodestone (normal Thaumcraft item)

Recipe:
Outside - Order Shard, Entropy Shard, Knowledge Fragment, Nitor
Middle - Flint

With only Thaumcraft (and NEI): It only accepts Order and Entropy Shards
With Thaumcraft and ThaumicEnergistics: I can use any shards in the recipe (like I can change Order Shard for another Entropy or Fire shard)

Mod List:
Minecraft: 1.7.10
Forge: 10.13.4.1614-1.7.10

AE2: rv3-beta6
CodeChieckenCore: 1.0.7.47
NEI: 1.0.5.120
Thaumcraft: 4.2.3.5

edit: Also It does not happen only with shards. Found one more recipe that asks for Silverwood Sapling but can be substitued for Greatwood Sapling (this recipe was Terrestrial Reformer from Automagy mod)

A little update after bit testing. I have noticed that all thaumcraft shards are receiving oredictionary tag materialAspectShard when Energistics mod is loaded.

So I used Minetweaker to add same oredict tag to dirt, and guess what... I can now substitute any shard with dirt as well.

Then I removed Thaumic Energistics and added manually the oredict tag to all Shards + Dirt... Issue is present.

So it doesn't look like its Thaumic Energistics doing it directly. Looks like Thaumcraft infusion is checking for oredictionary in recipes.

So closing this as not TE issue (maybe if possible just dont add oredict to the shards if you dont need to)