Can confirm on `OS X 10.11.6 (15G1212)` MC 1.11.2 (Modded, Major Mods: MCForge, Optifine). Also is still reproducible after switching modifier keys, this can be accomplished by going to `System Preferences -> Keyboard -> Modifier Keys` and swapping the `Command Key` with another modifier key.
==EDIT==
After looking at Minecraft's source code (through the minecraft forge sdk) I have determined this: This is most likely a problem with LWJGL 2 or OSX, I do not know if updating to LWJGL 3 will fix this problem. The way that minecraft handles stuff like `Ctrl/Cmd + a` is as follows: Minecraft queries LWJGL to determine if the 'a' key is pressed, then it ensures that the 'Shift' and 'Alt' keys are not pressed, then it checks if the 'Ctrl/Cmd` key is pressed this is done by checking the keycodes `219` (L_META/L_CMD) and `220` (R_META/R_CMD) if minecraft is running on OSX, on Windows it checks for keycodes `29` (L_CTRL) and `157` (R_CTRL). Minecraft does all of these checks by using the method `org.lwjgl.input.Keyboard#isKeyDown(int)`. LWJGL 3 uses GLFW for keyboard input and I have not found any issues reporting the same problem on there github issue tracker. This possibly could be fixed by updating to LWJGL 3 or it could be an internal problem with OSX, this is not a problem with Java since all keyboard handling in both LWJGL 2 and GLFW is done natively (with C/C++ code).
==EDIT 2==
People have mentioned reproducibility on Linux so this is most likely a problem with LWJGL2. Possibly the Unix Kernel but OSX has modified the Kernel enough that it is probably not the case.
Donovan
MC-73542
Can confirm on `OS X 10.11.6 (15G1212)` MC 1.11.2 (Modded, Major Mods: MCForge, Optifine). Also is still reproducible after switching modifier keys, this can be accomplished by going to `System Preferences -> Keyboard -> Modifier Keys` and swapping the `Command Key` with another modifier key.
==EDIT==
After looking at Minecraft's source code (through the minecraft forge sdk) I have determined this: This is most likely a problem with LWJGL 2 or OSX, I do not know if updating to LWJGL 3 will fix this problem. The way that minecraft handles stuff like `Ctrl/Cmd + a` is as follows: Minecraft queries LWJGL to determine if the 'a' key is pressed, then it ensures that the 'Shift' and 'Alt' keys are not pressed, then it checks if the 'Ctrl/Cmd` key is pressed this is done by checking the keycodes `219` (L_META/L_CMD) and `220` (R_META/R_CMD) if minecraft is running on OSX, on Windows it checks for keycodes `29` (L_CTRL) and `157` (R_CTRL). Minecraft does all of these checks by using the method `org.lwjgl.input.Keyboard#isKeyDown(int)`. LWJGL 3 uses GLFW for keyboard input and I have not found any issues reporting the same problem on there github issue tracker. This possibly could be fixed by updating to LWJGL 3 or it could be an internal problem with OSX, this is not a problem with Java since all keyboard handling in both LWJGL 2 and GLFW is done natively (with C/C++ code).
==EDIT 2==
People have mentioned reproducibility on Linux so this is most likely a problem with LWJGL2. Possibly the Unix Kernel but OSX has modified the Kernel enough that it is probably not the case.