This is a list of issues that, after careful investigation by Iris developers, have been determined to be unfixable on the side of Iris. Please don't open issues regarding them unless you have additional information.
These shaders conflict with shaders provided by Iris shader packs. See the core shaders compatibility document. This will need to be worked around on Botania's side by not using a custom shader, Iris cannot fix this.
Similarly to Botania, ComputerCraft uses custom shader programs for high-performance monitor rendering. Unfortunately, this doesn't work with Iris shader programs.
This will need to be fixed on the side of ComputerCraft once Iris has requisite code to accommodate the fix, which will be available once Iris has fixed this issue: Screens/monitors from Lifts mod turn black with shaders enabled. Once this issue is closed, CC:R will be able to render using its shaders to a custom framebuffer, then that framebuffer can be rendered to the scene with Iris's shaders.
The ComputerCraft: Restitched developers have implemented specific workarounds when using shader packs with OptiFine, but have not done so for Iris.
See: cc-tweaked/cc-restitched#1
Beyond potential issues with shader packs, Colored Lights isn't compatible with Sodium, and Iris requires Sodium, so Colored Lights cannot be used with Iris.
Multiconnect completely replaces the content of Minecraft's registries with pre-flattening block IDs when connecting to pre-1.13 servers. Since Iris shader packs use block IDs to determine block effects, and do not expect pre-1.13 block IDs when running on a post-1.13 Minecraft version, this breaks shader packs.
This notably results in solid grass blocks waving like grass plants, since in 1.12 minecraft:grass refers to solid grass blocks and in 1.13 minecraft:grass refers to the non-solid plant.
We can't fix this on our side, Multiconnect will ideally need to be changed to not disrupt registry content to such an extent.
See Earthcomputer/multiconnect#205
This is a fundamental limitation of how portals are rendered when shaders are enabled. They are composited on to the scene after rendering has completed, meaning that they cannot be rendered behind translucent surfaces like water.
This cannot be fixed by either Immersive Portals or Iris without completely reworking how portal rendering works with shaders.