We would simply say “mais avec prudence”.
I would rather translate by “avec précaution” or “en faisant attention”.

Though mais is not commonly followed by a comma, it is possible to do it to mark a separation of some sort (hesitation, short reflexion, a brief pause to catch the full attention of the person to whom the message is intended). This article from la banque de dépannage linguistique expands a bit more on the matter.

As far as your propositions go, both…

Mais, avec une certaine prudence.
Mais, avec quelque prudence.

…work and sound native.

In a daily context, my natural tendency would probably be:

Mais… prudemment!

Mais, les gens ont différentes approches du vocabulaire !¹

Dropping the adjectives altogether also work (perhaps even more efficiently, since the only concept then invoked is the caution):

Mais, avec prudence.

¹ …and many, even very different from each other, are equally valid.