It's natural to be caught off guard with thoughts on the unpreferred reality, and REACT/worry. I know we are observers and we aren't our thought's, but the habit sometimes makes us feel as though we were. I know a neutral/unconcerned reaction is ideal to move forward, but I personally seem to forget sometimes.
Naturally. None of us can maintain that 100% of the time, and life throws us all curveballs. The trick is when we recognize this is happening that we take action. We often learn through practice though and its really about making that new habit become so consistent that we spend more time in that observing space than in the thought space.
Long term through elevating your vibration. Also, becoming aware more often, will, over time desensitize you to it. Third, dealing with the strong emotions. The strength of those feelings is so strong it identifies us with it immediately, so healing some of those negative emotions (in your case it sounds like fear?) sounds beneficial. Don't only practice awareness of the thoughts, once you've reacted and are aware of that, you can also be aware of the feelings, sensations, etc.
It's easier to be a calm captain if the seas (subconscious) aren't rough and stormy. If they are, they have to addressed. Or, the opposite. Rough seas can make an otherwise unconscious captain, present and aware to the situation from which point, changes can be made.
I was literally doing a mental process in my mind last week where I labeled every unwanted thought as just a "thought" passing by, so I didn't attach any feeling to them. It was pretty efective, my reality reflected the shift quickly and some desired changes were taking place, however it was too complicated so naturally it stopped working after a few days. When I follow a method that is effective but a bit complicated it always stops working after a few days, cause it's more thinking in the end, so when I get caught off guard I go like "what was I supposed to do here?" and overthink.
What I do now is just let me thoughts be, even if they're negative, I don't fight them or try to ignore them, I acknowledge them because this is an inclusive universe.