98 Honda Accord manual transmission shifter in wrong gear

So my we have a 98 Honda Accord that we only drove for a couple days due to the fact that while it was being driven the transmission seemed to go out.
I do say seemed to because my boyfriend who was driving at the time claimed that the transmission had locked up. I personally ran through the list of symptoms and decided that it was not the transmission. However he insisted it was and replace it anyways. The problem is still the same.
What is happening is that the shifter is just pointing to the wrong gears somehow. When it is pointed to First it acts as if it’s in neutral, and when it is in neutral it acts as if it is in second or so. So because I’m a girl I don’t know what I’m talkin about, ;-), he insist now that it’s the clutch. I however beg to differ as there is nothing funny about the feeling of the clutch itself or any strange noises or anything of the sort. I believe it’s the shift cable, but since everyone is doubting me I to know how I can check this or if there are any other problems that could be causing this.