The anime episode showing Indra having Sasuke's eyes is a filler episode (see the list here). Trust the manga instead, which is canon. There are two reasons why the producers did changed it in the anime:
They got lazy, or they didn't have enough time to think of a unique mangekyo sharingan ability and animate the effects. So they slapped Sasuke's eyes onto Indra and called it a day.
Indra having Sasuke's eyes symbolizes how Sasuke is the reincarnation of Indra. Indra's personality, physical prowess, and intelligence were all passed down to him. So it makes sense that the MS was also passed down too.
Yeah, the will definitely be a few differences between the anime itself and the manga, for example, in the anime "one piece" there is a character named "Zoro," but in the manga, his name is "Solo." See the difference. Basically it really is for you to decide.
It's just because it's a filler arc and they didn't want to have to design a new pattern. It makes no sense for his to be the same as Sasuke's. Madara is also Indra's reincarnation, yet his pattern is different. Also, Sasuke doesn't awaken the mangekyou sharingan until after Obito implants Itachi's eyes in him, so Sasuke's sharingan isn't even really his own, and that means the theory that it's because he's Indra's reincarnation doesn't have any credence.