There are two likely causes for this issue:
i3 internal: Since version 4.11 (at least in some cases) the key symbols used with
bindsym need to be the ones that X recognizes when the given Modifiers are pressed. In your case with Alt+Print that means you have to actually use
bindsym Mod1+Sys_Req exec --no-startup-id scrot -zu
Because the key symbol of the Print key is actually
Sys_Req when when Alt is pressed.
Kernel configuration: It is also possible that the
MAGIC_SYSRQ configuration option is enabled in your Linux kernel. Depending on your distribution and kernel configuration, you may be able to check this with one of these lines:
grep CONFIG_MAGIC_SYSRQ /boot/config*
zgrep CONFIG_MAGIC_SYSRQ /proc/config.gz
With this option enable
Mod1+Print is caught by the kernel as part of the Magic System Request Keys, which all follow the pattern Alt+Print+[b-z0-9].
As it is caught by the kernel itself, the only thing you could do, would be to use a kernel that has this option disabled or disable it temporarily (until next boot) with
sysctl -w kernel.sysrq=0. (Credits for the
sysctl-workaround go to beanaroo)