Have been working 20+ years (in the US) and never heard anyone say anything other than "C-L-I"

The appropriate pronunciation of CLI is "terminal".

I say "command line" or "command prompt" when speaking to a Windows-based/minded audience. I drop the 'interface' part as there shouldn't be confusion over it.

I use "terminal" when speaking to a UNIX-based/minded audience.

I pronounce it "C-L-I" when thinking to myself.

C-L-I here.

I find that I generally pronounce 3 letter acronyms letter by letter but I pronounce four letter (or more) acronyms like words if I can, and only fall back to letter-by-letter if there's not an obvious word-like pronunciation. There are certainly exceptions ("SQL" being a notable one).

I go with c-l-i

I only say "C-L-I". It is an initialism (read the initials), not an acronym (read as a word).

I usually pronounce it "clee." I have never really heard anyone say it out loud though.

c-l-i for me.

I say c-l-i

When people pronounce SQL as "sequel" and CLI as "clee", I insist on pronouncing PHP as "fap".

C-L-I

Is it possible that they were saying see el eye with a strange accent?

see-ell-eye

1. See - El - Eye

2. Cly (like CRY)

see ell eye