If the same estimate is shown in two separate columns, using the -indicate- option, only one column of indicators is generated.
Code:
eststo first: reg y x1
eststo second:  reg y x1 x2
estout first second , indicate(vars=x*)
(correctly) produces
Code:
 ------------------------------------
               (1)             (2)            
                y               y          
 ------------------------------------
vars            Yes             Yes                    
 ------------------------------------
N               2967           2967           
 ------------------------------------
but
Code:
estout first second second , indicate(vars=x*)
produces
Code:
 ------------------------------------------------------------
               (1)             (2)             (3)   
                y               y               y   
 ------------------------------------------------------------
vars            Yes             Yes                   
 ------------------------------------------------------------
N               2967           2967         2967
 ------------------------------------------------------------
With a missing "Yes" in the third column

(I'm using Stata 15 with and estout *! version 3.21 19aug2016)

Since I do not know if Ben Jann follows this forum, his GitHub or can be reached through other channels I am also cross-posting this issue here https://github.com/benjann/estout/issues/18