Fourths are entirely acceptable between upper parts when a chord is in second inversion: (from low to high) E G C. There is a fourth between G and C, but it has been considered acceptable since renaissance times, since the bass forms consonances with the G and C (E-G is a 3rd, E-C a 6th). This fourth is always considered consonant.
On the other hand, a fourth from the bass is a dissonance. It is still often used as a nonchord tone. This fourth can also occur
on the beat. It is not uncommon to see, in Bach, something like C in the bass and in upper part F, then E. In this case C-F is a fourth, and F is probably an appoggiatura, an accented passing tone or a suspension. The F is not a member of the C chord, and it resolves to the E.
A special case of the above is the cadential 64 chord. Here you might see G (the dominant in C major) with C and E above it. This tonic chord in second inversion then resolves to the dominant; the C descends to B and the E to D. In this case, the C and E can usually be considered as suspensions, passing tones, or appoggiaturas.
Also, when a bass melody arppeggiates through chord tones, it is not uncommon for it to move into 2nd inversion for a moment. The fourths thus created are usually acceptable in baroque and later styles.
Also, I've noticed in much fugal music, the fourth shows up (always briefly) in sections with only two voices, perhaps even when both parts are in 1:1 counterpoint (in the same rhythm). Here the fourth is usually a fast chord tone or a quick passing tone used to move on to a sixth or third.
So, in Bach's fugues, you will find fourths everywhere... I hope this helped; if you already knew all this then just ignore it
.