Reigning world champion Sebastian Vettel had to settle for fourth in Sunday's Canadian Grand Prix after starting from the 32nd pole position of his career.
It was only the seventh time Vettel had clinched pole but failed to finish on the podium as Red Bull struggled with strategy.
Primarily, it was knowing which route to adopt with the Pirelli tyres that ultimately proved critical, with McLaren's two-stop plan holding sway over the those pitting just once.
Fernando Alonso and Vettel both paid the price, finishing fifth and fourth respectively when running first and second with eight laps remaining, the latter eventually making a late second stop after being caught by Hamilton that enabled him to pass the Spaniard.
"It was a difficult race, and we've quite a few things to reflect on and try to understand," said Horner.
"Ultimately we salvaged some reasonable points, beating Fernando.
"Lewis adopted a two-stop (strategy) and made it work. At one stage it looked like quite a bold thing to give up the lead.
"It was a very difficult strategic race. Things are complex (at the moment), that's for sure. Strategically it's very difficult to read.
"You are trying to make judgements through a race based on the feedback you have from your own car and the information you have around you, and it's tricky.
"Two guys that went on a one stop, one started 15th (Sergio Perez for Sauber) and the other at the back end of the top 10 (Lotus' Romain Grosjean) and they came out third and second.
"We qualified on pole, were in the lead on lap 15, yet ran into trouble seven laps before the end."
Asked whether the season had become too much of a lottery, Horner replied: "I think (the word) lottery is too harsh, but I would say it's certainly challenging."