yah they could mean something different, and it can be tricky in 古文 (classical Chinese)
1. 只、只是:
他只是在圖書館看書。 He just studies in the library.
他只在圖書館看書。 He studies only in the library.
2. 學、學習:學習 could just mean learning, then it is a noun; 學 could be followed by object
學習是快樂的。 Learning is delightful.
學跳舞是快樂的。 Learning dancing is fun.
3. 樓、樓層:
你住(第)幾樓? What floor do you live?
你住第幾樓層? (...well it's understandable)
4. 幾個、幾
"幾個" can be a question already, = how many
I could only think of some examples~