Why are katakana readings being rejected?

Though they sound the same it would be like writing eNGLIsh words with random caps. Yes, we can read the sound of it, but it is still not written correctly :wink:
There are rules to what word is written what way, though as mentioned katakana can be used as emphasis. But no pure hirgana word would be written half and half like that, so would always be misspelled.

Hope this answers your question. And if you struggle braking the habit there are scripts to let you mark answers as correct if you know you just typed it wrong (which is extremely useful even if you manage to stop doing this, as spelling errors happens a lot)

List of all user scripts: https://community.wanikani.com/t/The-New-And-Improved-List-Of-API-and-Third-Party-Apps/7694