I'm so sorry this happened to you. This would be completely unacceptable to me also. It would drive me crazy.
Bondo is a bad idea for this task for other reasons also. From another post where the person used Bondo to seal the seams in the slate:
I hope you never EVER have to take that pool table apart. Wax is the filler to use for the seams between the slate sections. [With Bondo,] those sections are going to come apart with jagged edges that will need to be sanded down to even make it possible to assemble the pool table again. The slate should be bolted and shimmed such that a dripping of wax in the seam, scraped off the top, is sufficient to yield a dead flat surface for the cloth to be laid upon. No offense intended, but if your table required a "fair amount of Bondo", you did it wrong. :(
And from another pool table mechanic:
[...] the problem with Bondo is that it can crack the slate when you try to disassemble the pool table the next time. I think bondo is a mistake to use. I've seen pool tables where people, in an effort to clean off bondo, sand the slate leaving waves in it. That makes for some interesting rolls. Not to mention beeswax is neater, faster and easier to apply and has all the give qualities you need.
I've also seen this type of thing (cloth discoloration) happen on pool tables where beeswax was used. In these cases, it was too much wax, and the pool table was in too much direct sunlight. It also discolored the cloth above it.
I do know that lots of folks and pool table mechanics DO use Bondo on slate seams and to repair chips in slate, and I've never come across any complaints that it caused discoloration in the cloth.
I wonder if your pool table installer used another chemical (perhaps to remove excess Bondo), and some residue remained on the seams and surrounding slate? Some parts of the discolored areas seem to be quite wide (e.g. is discolored on the exact seam, but in some parts, the discoloration appears to extend an inch or more to either side of the seam).
I'd absolutely call your installer to come back out and, at minimum, assess the situation, and at best, resolve this for you.