Blue Mana Shards either appear on certain fields to begin with, or as a result of Wave Sparks. Generally, they start with purple shells that need to be destroyed before mana can be harvested. The only shards that do not have shells appear on specific fields (but some do have shells like O1 and R4) and Corrupted Mana Shards.
Corrupted Mana Shards are yellow, large, and can only be fired at by gems with the "Structure" priority, or by clicking it while it is within range of gems in towers. Although they have an "endless" (actually 20 million) supply of mana, they significantly lower the damage of gems that shoot it, which also lowers the amount of mana gained per shot. These corrupt mana shards only appear in G1, O2 and X3.