The only way you can translate 原因 into hirgana is by saying げんいん. The kanji increases the differentiation in vocabulary, but if you're only using hiragana, you're going to get many words with the same hiragana. Think of だい... if you translated all the kanji into hiragana you'd get 代 - だい, 台 - だい、題 - だい etc, so you're not wrong :)

原因　is exactly [げんいん-gen in）] You're right! 現員　This is also[げんいん]　but, the meaning is [present members] 減員　This is also[げんいん]　meaning [reduction of staff] Keep up the good work!