Yup! The sentence does contain an error. The answer is NO.
"Two windows" is the subject of the sentence. This can be seen by twisting the sentence around:
"Two windows 'was' there..." "Two windows" is plural and takes a plural verb -- not "was" but "were."
The sentence should read: "There were at least two windows in each room."
Yup! The sentence does contain an error. The answer is NO.