I was experiencing the same issue. It turns out that the boilerplate code is the problem, because if you set freqQuery(queries: [[Int]])->[Int] to simply return [], it still fails some of the tests with timeout.

So, in the boilerplate, I replaced:

let queries: [[Int]] = AnyIterator{ readLine()?.replacingOccurrences(of: "\\s+$", with: "", options: .regularExpression) }.prefix(q).map {
    let queriesRow: [Int] = $0.split(separator: " ").map {
        if let queriesItem = Int($0) {
            return queriesItem
        } else { fatalError("Bad input") }
    }

    guard queriesRow.count == 2 else { fatalError("Bad input") }

    return queriesRow
}

with:

var queries = [[Int]]()
while let raw = readLine() {
    guard raw.count >= 3, raw[raw.index(raw.startIndex, offsetBy: 1)] == " " else { fatalError("Bad input") }
    guard let op = Int("\(raw[raw.startIndex])"),
        let val = Int("\(raw[raw.index(raw.startIndex, offsetBy: 2)..<raw.endIndex])")
    else {
        fatalError("Bad input")
    }
    queries.append([op, val])
}

And then all my tests passed. I'll submit this as a suggestion for them to fix as well. Cheers!