You are mixing up Caster Level and Spell Level. The formula for pricing magic items is generally
CL × SL × X gp
where X varies depending on the type of item. The Spell Level is as listed in the spell’s description, and seems to be the number you are using for both Spell Level and Caster Level. However, Caster Level is different: it is a property you get for having levels in the class that grants the spell.
Caster Level in most classes is equal to your level in the class. Some (so-called “half-casters,” e.g. paladin and ranger) have Caster Level equal to only half their class level. There are even oddball cases that use a different scheme for determining Caster Level.
Furthermore, each class gains access to spells of a particular Spell Level only at a certain Caster Level, which is usually higher than the Spell Level itself. For example, clerics, druids, and wizards only get to cast 2nd-level spells at Caster Level 3, while bards, paladins, rangers, and sorcerers get them at Caster Level 4. This is the minimum Caster Level for those spells for those classes.
Items are usually crafted at minimum Caster Level to keep the cost down, but the Caster Level must be at least the Caster Level at which the Spell Level may first be cast. For a 2nd-level Druid spell like barkskin, that is Caster Level 3.
With all of this information, it becomes clear what’s going on. You should be multiplying Spell Level and Caster Level, i.e. 2×3, but you are multiplying Spell Level with itself, i.e. 2×2. If you use 2×3×(50 gp), you get the 300 gp you see in the other table.
For a 3rd-level Cleric spell like water walk, a cleric needs a minimum of Caster Level 5 to cast that, so the cost is 3×5×(50 gp), or exactly the 750 gp you see in the table.
While not usually done, you can craft things with higher Caster Level. For example, you could craft a water walk potion with Caster Level 10 (assuming you have a Caster Level of 10 or greater), so that it lasts longer and is harder to dispel. This would cost 3×10×(50 gp) = 1,500 gp. This gets prohibitively expensive quickly, so most people stick to minimum Caster Level most of the time.
Do note that when you create a magic item yourself, you only pay gold equal to half the item’s base value. Be careful about whether a given table is giving you the crafting cost or the base cost. Also, some spells require extra materials or XP to cast, which is also reflected in their cost to create, and therefore also in their base cost.
Anyway, as for DMing and charging players who want to buy items, base costs are usually equal to the market value of the item. Most of the time, I strongly recommend just leaving it at that; the pricing isn’t anything like perfect but it works well enough and changes can have very unexpected results. Costs can be tweaked to represent unusual economic situations (particularly high demand for a given item, perhaps), but generally speaking that sort of thing should be done very carefully, and I recommend new DMs avoid doing so until they have a pretty good grasp of how the economy and system works (or doesn’t).