Learn Polish: Wiem, że to jest bardzo zła myśl. - I know that this is a very bad thought.

Most Polish nouns ending in a consonant are masculine, but there is a special group of feminine nouns that also end in consonants. Myśl (thought) is one of them, along with words like noc (night) and krew (blood). Because it is feminine, the adjective describing it must also be feminine, which is why we see zła instead of the masculine zły.

If myśl is feminine, shouldn't the sentence say "Wiem, że ta jest..."?

No, because of the grammatical structure being used. When you say "This is [something]" or "It is [something]", Polish always uses the neutral pronoun to in the phrase to jest, no matter what the gender of the following noun is. You would only use ta if you were attaching it directly to the noun, like in the phrase ta myśl jest zła (this thought is bad).

Why use wiem here instead of znam for "I know"?

You use the verb wiedzieć (conjugated here as wiem) when you know a fact, a situation, or when the verb is followed by a conjunction like że (that). You use znać (like znam) when you are familiar with a noun, such as a person, a place, or a language.

Why is bardzo zła myśl in the nominative case here rather than the instrumental case?