the first chord is C#,F#,D. This seems rather odd to me ...
As we can see this is an excerpt of the Toccata and Fuga of the Partita in E-minor.
I suspect the C# is a suspension
Like the 4th notes above the half notes are suspended in the toccata, Bach uses this motif in the fugue also as a suspension.
Yellow square = the motif with the suspended note and resolution.
Red square = the odd chord
Red circle = the chord note and (red stroke) the resolving chord tones.
In a fuga the 1st soggetto is in the tonic: E-minor = Dux
We may hear i->V6 (Em-B), but it could be also ii-V7 like in the 3rd entry!
(There are many music theorists pretending that Bach didn't write/think in chords and harmony but that he came from the polyphonic horizontal voicing concept ... I personally don't think so.)
Even this is a fugue and written in counterpoint you can hear already in this short motif of 3 notes the suspension: (both hands written in Bass clef !!!)
The suspended note (1st of the 2 tied notes) isn't part of the triad. The next tone, the resolving note helps us to define the chord:
The second entry of the subject is in B-minor (= i). The resolving chord is i-> V = Bm-F# (mind the inversions of the resolving chords!)
In bar 34 we have the 3rd entry of the subject in Em but in a different harmonisation: iv6-V2-V7-i.
Now to your question measure 41:
(I just wonder why you didn't ask about all these previous analogous situations!)
When the subject in Bm enters in the Bass (40) we have B,E,C#. B is suspended and resolving to A# -> A#,C#,E,F#: Yes! 1st inversion of F#7 (V7 of Bm).
(41) C# = suspension of the previous melody tone resolving to B: B,D,F# = Bm etc.
I know the following link was not part of your question, but it will help you to understand better what is happening in this Toccata and Fugue: