If the outside of 2 entities occupy the same space, the game doesn't know which one to render first, causing them to flicker. This only occurs while the player is moving. Once the player stops moving, the game will choose an order to render them (not necessarily the same order for all parts of the entity), and will keep it until the player starts moving again.
To replicate, summon 2 ender crystals half a block apart at the same elevation.
This can also happen with blocks. For example, a sign placed on top of another sign, or a glass pane in the "cross" position.
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That is called z-fighting and is probably "intended". Because when you have to objects at the same place there is no way for the game to tell which texture it should render in front.
Yeah, "there is no way for the game to tell which texture it should render in front" is the bug. It should just choose one of them.
Mainly that has to do with your textures. I have the same problem in Tekkit Classic sometimes. I looked into it and its just a texture bug. Nothing much to worry about.