Lt. Daniels tells McNulty of Kima's medical condition, including that she has had a "trach", but in the final scene of Kima in the ICU, she is clearly intubated orally (in her mouth). Once a patient has had a tracheotomy, it would continue to be used during that course of treatment.
When Bay teaches Dee to look after his many large tropical fish tanks, he points out his "tetras". However, these are 3-spot gouramis.
When Rhonda Perlman and Jimmy Mcnulty are arguing on the street Dominic West's British accent can clearly be heard.