No not as long as the boil is not causing any acid to spew out. In fact a light boiling or I should say a sizzling sound should be heard. You need a high enough charge rate of about C/10 on FLA batteries to prevent stratification. In other words stir the acid up so it does not settle at the bottom of the jar and the water on top, aka stratification.
If you don't hear a little bubbling sound at the end of a charge that would be bad. Lead acid batteries fail rapidly if not regularly fully charged and it is best to bring flooded cells into the gassing voltage range and the end of each full charge.
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