is
The issue is, is that we need to clarify what it is.
The sentence is a colloquial filler construction in spoken English where 'is' appears twice consecutively after 'the issue' — the first as part of a setup phrase, the second as the main verb of the clause that follows.

Meanings (pronounced /ɪz/)
the third-person singular present of 'be' — denotes existence, identity, or a state
- She is a doctor.
- The sky is blue.
the same word, used twice in colloquial spoken English to introduce a clause after a setup phrase ('the issue is, is that...')
- The thing is, is that we're running out of time.
- The point is, is that nobody asked.
Word origin
From Old English is, the third-person singular present of bēon/wesan ('to be'), from Proto-Germanic *isti, from Proto-Indo-European *h₁ésti. The English copula 'be' is one of the most ancient and irregular verbs in the language — its forms (am, is, are, was, were, been) come from no fewer than three separate Indo-European roots that fused over time.
Fun fact
The 'is is' double — as in 'the thing is, is that...' — is so widespread in spoken American English that linguists have given it a name: 'ISIS' (the 'is is' phenomenon, predating the militant group). Despite being condemned as ungrammatical in writing, it shows up in the speech of educated people millions of times a day, suggesting it serves a real cognitive function as a sentence-restart mechanism.