When it comes to reading magickal symbolism, I’m in the same school of thought as you, @phoenix_dawn- that not everything automatically carries deeper symbolism. The best way to tell if something is worth reading or not lies in your intuition- and it sounds like this encounter really was something out of the ordinary (and I don’t blame you- that would have startled me too! 
)
Also, there’s the fact that this experience occurred while you were casting a spell and it landed on your altar aka your sacred space- it wasn’t something you happened upon during your normal day, it has a direct tie to magickal working.
These things paired with the fact that you have an ongoing strange situation and that your intuition is nudging you about it all lead me to believe that this is something worth looking into 
So assuming there is a message you are meant to find, there are a few ways you could read the magickal symbolism here:
- First, by looking at the Fly
Various sources take difference stances on this one, so I’d recommend checking out a few and seeing if anything resonates with you. There’s Spirit Animals: Fly Symbolism, Native American Fly Symbolism, Spiritual Meanings of Flies, etc.
In general, although a few places offer a positive spin, flies are signs of things like disease, death, annoyance, plague, suffering, anger, and war.
But in my experience, traditional readings often take a backseat to personal readings- especially if this is a sign meant for you. What are your personal readings about flies, Phoenix? Is there someone you associate with flies, or whom reminds you of them?
- Second, by examining the state of the fly
This one is pretty straightforward- it was dead. That’s the most obvious sign of death you can get- but is it death as in the most basic sense, or is it more like Death the tarot card, a sign of change?
Again, as a sign meant for you- your interpretation of this will carry the most weight here.
- Third, trying to relate the dead fly to the spellwork
The fly could be connected to the truth spell you were working or to the situation at large (that was causing you to cast the spell).
If I was casting a truth spell and a big fat fly dropped dead on my altar, I would take that to mean that my suspicions are confirmed- that someone is “plaguing me” so to say, buzzing about my business and spreading negativity.
These are just my thoughts and how I would break down the reading shared with the hope that they might help you- but as always, if this sign was meant for you, you are in the best position possible to piece out the meaning. Trust your intuition! 
Good luck, Phoenix- I hope you can figure out what is going on and clear the negativity soon! 
Blessed be!