Hi Aggeliki,
Your mobile phase can certainly be that low, however, some columns will have shortened life-spans at low pH's and it may end-up damaging them in the future. Of course, I am not the expert on your columns and this may be completely fine!
That leads me to my next question, what column are you using and what are your mobile phase additives?
Mind you, if your mobile phase was actually at a pH of 1.9, your analytes would have been fully protonated and eluted correctly on both runs. Interestingly, your second analyte does not change retention which makes me believe that there was some sort of change in pH to allow for this compound to elute later. Is there any possibility that the standard analyte is sensitive to anything or was potentially contaminated? Some standard analytes can decompose under particular conditions like exposure to UV light or spending too much time in water.
Tyler