I have multiple clarinets that double on Bb and A instruments. Instead of having it numbered as: Clarinet I in Bb and A & Clarinet II in Bb and A, it numbered it as: Clarinets I in Bb and II in A & Clarinets III in Bb and IV in A.
How do I fix this?
Engraving Options—Staff Labels—Numbering—Numbering for similar instrument with different transpositions: Number separately.
This will give you:
Clarinet in B♭ 1
Clarinet in A 1
Clarinet in B♭ 2
Clarinet in A 2
That isn’t a general solution because it doesn’t properly handle the case where your doublings are not homogenous. Like for example, if only your 2nd clarinet doubles on an A, it’ll be Clarinet in A 1, not Clarinet in A 2.
I’ve complained about this before.
The way dorico handles it is fundmentally wrong. PLAYERS should be numbered, not instruments. The 2nd clarinet or 3rd horn is always such no matter what they’re holding at any given moment.
The simple work round is double your first clarinet as well, but never use the Cl in A 1.
Not always. Show me a score where Flute 2 doubles “Piccolo 2” or Oboe 2 doubles “Cor Anglais 2”. 
Numbering by player is not always correct. As per Gould (page 531 in Behind Bars), the last player is usually the first two double. If there’s three flautists and two are doubling piccolo, Flute 3 = Piccolo 1 and Flute 2 = Piccolo 2.
The except is when two players both double the same instrument. In this case, they keep their player numbers, e.g. Clarinet 1 = Bass Clarinet 1 and Clarinet 2 = Bass Clarinet 2.
Ideally, Dorico should eventually provide greater control for the automatic numbering to cover the cases above.
The “number separately” option worked for what I needed. Thanks.