“Sir, I think we have an issue.”
You're watching an action movie. A soldier on a battle ship is looking at a radar screen and sees some objects flying toward the ship. She says this to the commander.
Sir, I think we have an issue.
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I think (clause)
In spoken English, you can say "I think ___" before the idea that you're thinking.
I think I'm finished.
I think she's coming.
In formal writing or when you're speaking carefully, you should use "I think that ___" instead:
I think that we need to do a lot more testing before we release it to the public.
In the military, soldiers call higher-ranked male officers "Sir":
Sir, we've reached the target.
A higher-ranked female officer might be called "Ma'am", or "Sir", depending on the customs of the organization.
We have an issue.
When a problem occurs that affects a group of people, you can say "We have a problem."
Uh oh, we have a problem.
The phrase "We have an issue" means the same thing, but it's a little more restrained. In other words, an "issue" doesn't sound as bad as a "problem".
Hmm... we might have an issue.