Merlin sometimes uses Putt-Putt's calculator as a battery for his gold machine, and Putt-Putt needs to get a battery for him to get the calculator back. The voltage of the battery changes every game, but is usually more than nine volts. The average calculator battery delivers 3-6V, so there is no way that Merlin would be able to use it on his machine if it needed over 9V.
The battery maker in the future shows a bulge going through the pipe into the battery every time Putt-Putt adds voltage, and the bulge going the other way when Putt-Putt takes voltage off. In real life, if a battery machine like this was even possible, the entire chemical composition of the battery (or cell) would have to change for the nominal voltage to change. In other words, simply putting more juice in the battery won't increase its voltage. Additionally; although this was clearly left out to make the game easier; when constructing a battery, there are other quantities to worry about besides voltage (such as energy, charge, C-rating for rechargeable batteries, etc.).
The Triceratops couldn't chew as shown in the game - they used stones to grind their food.
Sir Poundalot charges a nickel for the armor centuries before it was a form of currency.
Merlin uses the term "Volt" in the Middle Ages, at least three centuries before Alessandro Volta (for whom the unit is named) was even born.
In the prehistoric area, Putt-Putt meets a Brachiosaurus, an Apatosaurus, a family of Pterodactyls, and a Compsognathus (all of which lived during the Jurassic era); as well as a Triceratops and a Tyrannosaurus Rex (both of which lived during the Cretaceous era). The Jurassic and Cretaceous eras were millions of years apart. Additionally, Wheel shouldn't exist for at least another 65 million years, and Mr. Bird shouldn't look like a modern bird at all.
King Chariot and Princess Chassis are modeled after vehicles that weren't common until a few hundred years after the Middle Ages.
It isn't possible to complete the game if the lunch-box is in the prehistoric era and the history report is in the future. Both paths require Putt-Putt to buy something with a nickel, and after the time portal opens, he only gets one.
In some games, Merlin asks Putt-Putt for a battery with "nine volts of power" (the number changes every game, but that is irrelevant). When he creates a battery in the future, Putt-Putt uses the term "volts of power" as well. The volt is not a unit of power - it is a unit of potential difference. Furthermore, power is usually not a quantity that is important when choosing a battery; at least, not as important as charge or voltage (potential difference).