This is a good point. And a very good example too! I had the same problem during the first year or so of my relationship, and it took me a long time to learn that when my boyfriend sounds like he doesn't want to talk to me, it's just because he is tired or stressed out and it has nothing to do with me or the relationship. It's most likely that your INFJ feels somewhat responsible for the less-than-happy conversation and thinks she must be doing something wrong, or that you are mad at her, or you're no longer happy about being with her.
It takes time -- perhaps quite a long time -- and a lot of reassurance that your tone of voice is NOT an indication of your level of interest before your INFJ will realize that this is really the case. I know this sounds stupid, but Ni + Fe is programmed to take into account all non-verbal signs as well, which includes tone of voice, choice of words, conversation flow, length of conversation, time of conversation, what you talked about in the last conversation, yes, everything, to make sure they understand all there is to understand. Taking things literally is very unnatural and a very foreign concept for INFJs. Over time, if your behavior is consistent, she will learn to trust you and understand that there is really NO hidden meaning.
INFJs are very, very slow to open up, and very, very slow to trust. My boyfriend said this as well: "One little slip and you're that sad?" Well, the INFJ tends to interpret something like this as a sign that deep down you don't want to do what you have been doing so great for months, and the 'slip' is your 'true self' surfacing. And, of course, this leads to all sorts of crazy thoughts like how you might not be compatible or how she is trying to change you too much and will eventually make you unhappy or how it's not going to work.
Wow, this post makes INFJs sound neurotic
One thing I think I should mention is a little note on the Fe-language. If you mention right at the beginning of the phone call that you had a rough day and are tired she will tune in to that. (How does this work? This is Fe on your part anticipating that the felicity of the conversation will be affected and asking the other party to adjust. She will "adjust" to it by not taking the 'tired tone of voice' personally and paying more attention to comforting you and making sure you are happy. All this is natural for her, perhaps even unconscious. "Our happiness" is the goal, so if you can make her understand where you are coming from, you have created the "us" and she will do everything to make "us" happy)
Similarly, if you have to say no to something, break your word, cannot spend time with her, or do anything that she will feel negatively about, make sure you tell her about the 'fix' immediately after the bad news. "I know we were supposed to go out tonight, but there's this report at work that needs finishing and my boss wants it now. So how about we do popcorn and dvd later instead? You get to pick the movie!" This shows consideration for the "us" and she'll be all sweet and loving when you get home