“I like your sister, she’s really funny.”
“Your sister seems a little funny.”
On the surface these two sentences may seem to have similar meanings. You will notice a difference in tone (the word stress in the sentence) however. “Funny” can mean “comical or humorous, able to make someone laugh” or it can mean “strange, weird, off-putting.”
This second definition is less common, it is used when you are not 100% sure if there is a problem with a person, thing or situation – but you get a feeling something is wrong.
“I’ve got a funny feeling about this.” Is a common phrase to hear someone say in a horror movie as they enter a scary situation.
“My science teacher seems funny. Not funny ‘ha,ha’ , funny ‘weird’.” Is the way you might describe someone that seems strange or unusual. The “Not funny ‘ha,ha’ , funny ‘weird’” part is sometimes added for clarification.
“My shoulder has felt funny since the baseball game last week,” would be a way to say that there is a little pain, or an unusual feeling in the shoulder.
It’s important to note that most things that are comical or humorous are also “funny” and enjoyable because they are strange or unexpected. So the definitions are actually related.
The best way to tell the difference is just by context and tone.