In a homomorphic scheme, you have a machine A (trusted), which encrypts some data and sends it to machine B (untrusted) and B then does operations on the data a

In a homomorphic scheme, you have a machine A (trusted), which encrypts some data and sends it to machine B (untrusted) and B then does operations on the data and returns the results to A, which decrypts. This attack is on machine A, not machine B. The "leak" happens as the data is being encrypted. They're sidechanneling a machine that has the plaintext on it.