Error 1: You wrote Ea0 two times, but surely meant to write Ea1 in the second sub expression.
Error 2: Since the && is evaluated before '||, your loop will only end if both sides are false.
What you are describing above is another expression, where you want all sub expressions to hold true for the loop to continue:
while ((Ea0 >= 0.01) || (Ea1 >= 0.01)) && (Sr >= 10^-4)
Note the extra parens around the EaX expressions to specify that both must fail for the loop to end. If you want any sub expression to end the loop, replace '|| again by &&.
See http://www.mathworks.com/help/releases/R2016a/matlab/matlab_prog/operator-precedence.html for operator precedence.
