"There are nine tables."
Numbers (and kanji in general) have different readings in Japanese. The character for nine (九) can be read as きゅう or く, and these are called the On'yomi, the readings borrowed from Chinese pronounciation, but it can also be read ここのつ, which is the Kun'yomi, the original Japanese pronounciation. If you use a number to count nouns, you need to use particles called “counters”. In this case we have the つ particle, which is the particle for objects, and here the Kun'yomi reading is needed.
Yes, one all the way to ten, and perhaps beyond to 99. That is how it is in Korean, language closest to Japanese. One set of counting in original native Japanese, and another set from Chinese. In English, although not used in counting per say, we have similar thing happening with Latin adjectives, duo, trio, quadro, penta, etc.
can anyone explain to me why i can't use 九つテーブルがあります? I'm still confused with the placement of that
It could also be that Duo insists on using the Kanji 九 so you learn it and familiarize yourself with it, that was the case in some previous lessons.
As for は, it can be used grammatically, but sounds very odd. It gives off the feeling as if you're trying to say "As for these nine chair, they exist (and other chairs don't)." You generally want to use が when you're using あります to say something exists .