Prelude:
A couple weird measures. Most notably 3 and 12. For 3 and 7, the use of the German +6 is really nice in terms of building tension, but are followed by confusing chords, C˚ and Eb˚7, respectively. I kind of see what you're going for on 7, which is why I think that one is okay; it seems like you're eliding a cadence which is clever. 3 doesn't have the same treatment.
Measure 12 is just a bit awkward because of the tritone leap to the top note.
In general, I think the fact that this entire Prelude sounds like one voice makes it sound more like the first period in a two-period structure with something else added the second time. Just feels a bit empty.
Fugue:
In two voices, parallel dissonances (where two non-standard intervals are consecutive) are not "wrong", but they do sound awkward (they would be wrong in Renaissance counterpoint, however). Places like beats 3 and 4 in m. 20 just sound out of place because of it.
The same rule applies with parallel 4ths. Beats 3 and 4 in m. 31 are an example of this.
Speaking of m. 31, why did you go back to two voices at m. 30? The episode isn't super long, but it kind of unnecessarily loses a voice.
m. 26's first beat confuses me, mostly for the major 9th between the bottom two voices.
The fugue's general structure is also a bit weird:
Subject - m. 15
Answer - m. 19
Codetta - m. 22 (this is too early; you have one more measure of subject to get through).
3rd Voice - m. 26 (why does the soprano suddenly have the answer again?)
I could go on, but it seems like it needs a little more direction.