I believe I understood your question a bit. I will try to elaborate on that.
If you check out the episode of the Nine Tails attacking the Leaf Village, you must have noticed different age groups of various characters. Kakashi, Gai, and Asuma were depicted as teenagers. There is even a clip where Itachi was holding the infant Sasuke on his lap, assuring him that he would always protect him. Itachi was around 10-11 years old. By this, I can conclude that Kakashi was an elder to Itachi.
In your question you stated that:-"Obviously, he[Itachi] didn't know about Obito/Kakashi",I would like to highlight something which could contradict with your statement. Itachi did know about Kakashi as he was a prodigy in his age. Getting Sharingan after Obito's death made him a source of attraction.
By then, Obito was out of the picture completely [since everyone assumed him to be dead]. At the beginning of the Shippuuden episodes, Itachi called Kakashi, "Copy Ninja", while he fought against him. Now, coming to your question, Itachi couldn't figure out the man behind Tobi's mask. Because of his boastful nature and strong power, Obito made Itachi believe that he was Madara. Obito's calling himself Madara depicts his deceptional and boastful behavior.
With this, I can say that there is no plot hole anywhere.
As debal said, both Kakashi and Itachi were in ANBU group.By this we can conclude that both knew each other.
To make it clearer we can list all current know Mangenkyo users and how they have or might have obtained it.
Itachi - It is thought he killed Shisui but did not. Very likely he witnessed Shisui's death. I can think of one scenario but it's just a speculation.
When Itachi saw Shisui for the last time, he had MS activated. I think Shisui used Kotoamatsukami on Itachi and made Itachi to kill Shisui. Itachi can't remember it, 'cause Shisui used Kotoamatsukami, so the victim isn't aware that they're being controlled. That way Itachi got his MS and Shisui wanted him to protect Konoha.
Shisui - Unknown. But seems unlikely he murdered anyone as he showed a great deal of self sacrifice do kill himself rather than have his eyes fall into the wrong hands.
Sasuke - Did kill Itachi and he witnessed his death.
Kakashi - Got his MS after killing Rin;although he came to know about his Mangekyou at later stages
Obito - Saw Kakashi killing Rin;which triggered his MS