import java.util.Scanner;

public class Main {

  private static void checking(double a){
        if(Math.sqrt(a)%1==0){
            System.out.printf("%.0f",Math.sqrt(a));
        }else{
            System.out.printf("%.4f",Math.sqrt(a));
        }
    }

    public static void main(String[] args) {
        Scanner scanner = new Scanner(System.in);
        System.out.print("Сколько чисел хотите ввести: ");
        int a = scanner.nextInt();

        double[] b = new double[a];

        for (int i = 0; i < b.length; i++) {
            System.out.print("Число " + (i+1) + ": ");
            b[i] = scanner.nextDouble();
        }

        for(double c : b){
            System.out.print("Корень " + c + " = ");
            checking(c);
            System.out.println();
        }
    }
}

I'm not sure what's causing the runtime error, but I tried your code on an online compiler and this was the error message I got:

Exception in thread "main" java.util.NoSuchElementException
    at java.base/java.util.Scanner.throwFor(Scanner.java:937)
    at java.base/java.util.Scanner.next(Scanner.java:1594)
    at java.base/java.util.Scanner.nextDouble(Scanner.java:2564)
    at Main.main(Main.java:22)