Version Found: 2015.3
The example design generated by the High Speed SelectIO Wizard does not check for alignment of data between the bit slices, it only check on an individual channel basis.
Note: this Answer Record should not be viewed in isolation. For all other known issues and to see what version of Vivado / High Speed SelectIO Wizard these issues have been resolved in, please refer to (Xilinx Answer 64216)
This issue is resolved in version 3.0 of the High Speed SelectIO Wizard, available in the 2016.1 release where the testbench implements the check.
To work around this issue in older versions, you can add the following comparison code at the top level of the example design or within the test bench.
The following example is a simple check to make sure pin0, pin1, pin2 and pin3 all match.
In this example pll0_clkout0 is used for driving the fifo_rd_clk_0: