You have resource restrictions on all three resources, which limit them to a maximum of two produced, until you discover the appropriate technology advance to remove the restrictions.

Each resource type has a particular technology advance that needs to be discovered to lift its respective restriction; for Nutrients, you have to discover Gene Splicing, for Minerals you have to discover Ecological Engineering and for Energy you have to discover Environmental Economics.

Prior to these discoveries, most squares will suffer from these Resource limits, however there are two exceptions to this general rule; the central base square never has Resource limits, it is fully exploitable with regards to all three Resource types. Secondly, Resource Special squares produce the maximum possible of their special resource, without regards to resource limits.

So, for example, if you found a Base on a Resource Special for say Nutrients, you will get the +2 Nutrient bonus in the Base square, regardless of Resource limits. If you have a resource special for Nutrients within a Base's production radius, and work it with a Citizen, then it will also produce to its full capability, but only with regards to the resource special. So a Nutrient Special square at 3000+ metres will produce +2 Nutrients [due to the Nutrient Special] prior to discovery of Gene Splicing, but it will only produce 2 Energy [rather than its potential 4 for elevation] until you discover Environmental Economics and lift the Energy Resource limitation.

Just as a minor correction, Bore Holes produce 6 Minerals and 6 Energy, not 8, once the Resource limits have been raised - prior to discovery of the appropriate Technology advance, they, like any other square, suffer from Resource limitations as well, so without either of the proper Technology advances needed, they will produce 2 Minerals and 2 Energy. Of course, Boreholes, like any other square, have these restrictions lifted if they are a Resource Special square.

For example, a Borehole which is a Mineral Special square will produce the maximum possible Minerals [8 in this case] even before discovery of Ecological Engineering; likewise it will produce 8 Energy if it is an Energy Special square even prior to discovery of Environmental Economics.

This effect makes Resource Special squares doubly important and valuable - not only do you get the intrinsic +2 resource from the Special, but you also have the Resource restrictions lifted for that particular square, so that it is fully exploitable with regards to whatever resource it is a Special Resource square for...

These effects [the Resource limitations] make planting Forests on those squares especially useful before the Resource restrictions are lifted. For example, a non-Rocky square with a Mineral Special resource will produce 4 Minerals with a mine [if Flat] or 5 Minerals with as mine [if Rolling] and suffer the limitations with regards to Nutrients and Energy production. Planting a Forest however will garner you 4 Minerals for the square, along with 1 Nutrient and 1 Energy. Building a mine will take you 8 turns [and another 1 or 2 turns for the road you need to gain the maximum production from the Mineral Special with a mine] while planting the Forest takes only 4 turns.

So.... building a farm and a mine and a road on a Flat Mineral Resource Special square will take you 4 + 8 +1 turns, 13 total, to garner you 1 Nutrient [even if a Rainy square, only 2 Nutrients], 4 Minerals and no Energy, while planting a Forest will garner you 1 Nutrient, 4 Minerals and 1 Energy after only 4 turns. Pretty significant difference in amount of time spent to exploit that square!

Especially early in the game, when speed of development is paramount and the Resource restrictions are in place, one needs to think long and hard about whether or not planting a Forest [fast] is a better resource deal than building a Farm+Mine+road or a Farm+Solar combination [both much slower].

Personally, I find Minerals to be a more important resource early on, so I usually plant the Forest, rather than building a Farm+Mine+road or Farm+Solar combination, especially in Flat or Rolling squares below 2000+ metres. I prefer a 3 Nutrient, 2 Mineral and 1 Energy Forest square on a Nutrient Resource Special square rather than the 3 or 4 Nutrient, 0 or 1 Mineral and 1 or 2 Energy from a Flat or Rolling Arid or Moist square with a Farm+Solar....

The major exception to my rule about planting Forests applies to Energy Resource Special squares at 3000+ metres of height [where you get 6 Energy from a Solar collector rather than the 3 Energy from a Forest, and Mineral Special Resources on Rocky squares, where you can get 7 Minerals with a Mine+Road, rather than the 4 Minerals you would get from having to both reduce the Rockiness and plant a Forest [8 turns to level and 4 turns for Forest].

Bottom line in answer to your question is that you can not fully exploit a square's potential production maximum until you discover the proper Techs needed to remove the Resource limits for *each* of the three Resource types. Until then, one [at least] type of Resource will be "blacked out" and the square will not produce the maximum possible Resources.

Rich