No, there's no mistake, but there is a piece missing. Specifying the InputFormat when you construct a datetime only controls how the input data is interpreted. It does not affect how the resulting datetime is displayed. For that you need to set the Format of the datetime. If you want the data to be displayed the same way it was interpreted, specify the same format for both InputFormat and Format.
fmt = 'yyyy-MM-dd HH:mm:ss:SSS';
dt = datetime({'2023-06-27 16:20:00:036'}, ...
'InputFormat',fmt, ...
'Format', fmt, ...
'TimeZone','America/New_York')
Or you can set the Format property of the datetime after it is created.
dt2 = datetime({'2023-06-27 16:20:00:036'},'InputFormat',fmt,'TimeZone','America/New_York')
dt2.Format % Note this is not the same as fmt; it doesn't include fractional seconds
dt2.Format = fmt % Set the Format on the already created datetime
In any case, this is a display issue; even if the datetime doesn't show that it has the fractional seconds, it does as you can see by asking for the seconds component of the datetime.
dt3 = datetime({'2023-06-27 16:20:00:036'},'InputFormat',fmt,'TimeZone','America/New_York')
second(dt3)
