What does "% is unavailable: Use truncatingRemainder instead" mean?

The % modulus operator is defined only for integer types. For floating-point types, you need to be more specific about the kind of IEEE 754 division/remainder behavior you want, so you have to call a method: either remainder or truncatingRemainder. (If you're doing floating-point math you actually need to care about this, and lots of other stuff, or you can get unexpected / bad results.)

If you actually intend to do integer modulus, you need to convert the return value of CMTimeGetSeconds to an integer before using %. (Note that if you do, you'll lop off the fractional seconds... depending on where you're using CMTime that may be important. Do you want minutes:seconds:frames, for example?)

Depending on how you want to present CMTime values in your UI, it might be better to extract the seconds value and pass it to NSDateFormatter or NSDateComponentsFormatter so you get appropriate locale support.

CMTimeGetSeconds() returns a floating point number (Float64 aka Double). In Swift 2 you could compute the remainder of a floating point division as

let rem = 2.5 % 1.1
print(rem) // 0.3

In Swift 3 this is done with

let rem = 2.5.truncatingRemainder(dividingBy: 1.1)
print(rem) // 0.3

Applied to your code:

let totalSeconds = CMTimeGetSeconds(self)
let hours = Int(totalSeconds / 3600)
let minutes = Int((totalSeconds.truncatingRemainder(dividingBy: 3600)) / 60)
let seconds = Int(totalSeconds.truncatingRemainder(dividingBy: 60))

However, in this particular case it is easier to convert the duration to an integer in the first place:

let totalSeconds = Int(CMTimeGetSeconds(self)) // Truncate to integer
// Or:
let totalSeconds = lrint(CMTimeGetSeconds(self)) // Round to nearest integer

Then the next lines simplify to

let hours = totalSeconds / 3600
let minutes = (totalSeconds % 3600) / 60
let seconds = totalSeconds % 60