I thought about this too and you're right about it being different. Indeed if you look at Sasuke's MS as 3 pointed ellipses overlapping, it does indeed match the 3-tomoe MS pattern. If really you look at it differently, you could even see the black sections as the 'tomoe' where they would be 3 pairs of curved triangles each connected by a thinly outlined diamond..... but no one really looks at it that way. However, clearly Shisui's MS breaks that pattern for sure. I tried to figure out in my head how 3 distinctly shaped tomoe could form a MS pattern resembling 4 tomoe, but no matter how you slice it, it doesn't work. Clearly Shisui's is made up of a 4-tomoe pattern.
Now with this information, we would have to assume one of 2 things: Either Shisui evolved a normal sharingan with 4-tomoes, which has never been proven to exist and is extremely unlikely, or his MS was unique and formed a 4-tomoe pattern simply due to its special nature. In reality, we have to assume it is that latter and perhaps we can attribute it to either his unique MS technique or perhaps to how he obtained the MS itself, but either would be speculation.
Whatever the explanation, there is one thing that aggravates me more than the 4-tomoes.....the fact that it is so similar to Itachi's! I mean if it only had the 3 tomoe, the only way it would differ from Itachi's would be that it has a regular black pupil when Itachi's is red.... It really irritates me that Kishi would put so little effort into making Shisui's unique. I mean I really like Itachi's, Kakashi's, Madara's and Izuna's, but Kishi went way overboard with Sasuke's and made Shisui's crap..... Now I'm really wondering how Kishi will go about Sasuke's EMS....