If the orange pitches actually produce the correct sounds, you need to configure a transposition in the Score Manager to put them on the staff. The other (less likely) option would be to create a Percussion staff Percussion Layout to place the pitches.

Actually, the notation is four (4) octaves too low.  The sounding range is C6 to C7, but notated C2 to C3 (two octaves, up to one octave, below middle C).  The Clef tool will not change the clef, and the maximum transposition is + 2 octaves.  They sound, but what is supposed to be C on the second ledger line above the treble clef is written as Middle C.  And there is no access to crotoles using percussion notation - only standard notation gives access - undertandable given crotales are tuned percussion.  Sounds like a Finale software problem for which there is no fix other than them fixing the s/w.

What sound set are you using? I do not see crotales in any of the Garritan sets I am familiar with.

The Finale MIDI sounds automatically transpose the sound, but if you wanted you could presumably adjust the transposition further via the Score Manager.

EDIT: Okay, I found the Crotales in the Garritan Instruments for Finale. I can notate them from middle C to the C above and they sound two octaves higher (regular treble clef).

Have you tried choosing all your Crotale notes and then pressing the 9 key to transpose the written notes by octaves up into a suitable written range? (In Finale 26 and I think in 25 as well, instruments that transpose at an octave or multiples thereof do not change their written pitch whether in Transposed or Concert scores.)