As has already been said, this did come up before. On that occasion, I suggested "substantive objection", and I still think it's a valid translation. Here is the evidence I provided last time (that is, on this term; the question also included "observación de oficio", for which I suggested "official objection").

"Observación" means, I think, a comment on a defect: an objection. I have met it in this sense before, particularly in Latin American official documents. "Observar", by the same token, is to raise objections. This is clear from the following later section in the Chilean law:

"Artículo 18.- Observaciones a la solicitud de anotación: En el caso que el Director respectivo observare la solicitud por estimar que existen impedimentos de forma o fondo para conceder la inscripción, el solicitante tiene el plazo de 30 días para subsanarlas. Una vez que se cumpla con la observación, o una vez terminada la tramitación de la solicitud anterior, la solicitud podrá ser aceptada o rechazada."
http://www.derechomarcario.cl/nueva ley/Borrador Minecon-INA...
http://web.ua.es/es/contratos-id/documentos/ip-tango/compara...

So "cumplir con la observación" means to take the necessary action to meet the objection.

One of the basic dictionary definitions of "observar" is "advertir, reparar". I'm really suggesting that "observación" here means "reparo".

Here's another example of the use of the word in Chile, in the context of trademark registration. I think the context makes the meaning clear:

"4) Oposiciones y observaciones de fondo: realizada la publicación, comienza un plazo de 30 días hábiles para que aquellas personas que se sientan afectadas por la solicitud deduzcan oposición al registro. Vencido este plazo, el INAPI comienza el examen de fondo de la marca, donde analiza si esta incurre en alguna causal de irregistrabilidad, reguladas en los artículos 19 y 20 de la Ley 19.039.
En caso de haber oposición o alguna observación de fondo de INAPI, el solicitante tiene 30 días hábiles para contestar (que, como indicamos, debe ser a través de abogado). Vencido este plazo, haya contestado o no, INAPI resolverá si acepta o rechaza el registro."
http://www.legalchile.cl/que-tengo-que-hacer-para-inscribir-...

"De fondo", by contrast with "de forma", is normally rendered in English as substance vs. form, as in defects of substance and of form. See here, for example:

http://thelawdictionary.org/defect-of-substance/

So I think "substantive objection" is right for "observación de fondo".

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Note added at 6 hrs (2014-06-21 16:14:47 GMT)
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Note that "observación de fondo" appears to be something emanating from the patent office itself, not from a party involved in a patent application. So I don't think it can be a submission. In clause 13 of this law it says "Cuando, además de la oposición, se hubieren dictado observaciones de fondo a la solicitud de registro..."
http://www.alessandri.cl/abogados/wp-content/uploads/sites/4...

"Dictar" implies a ruling from the patent office itself.

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Note added at 2 days2 hrs (2014-06-23 11:57:44 GMT) Post-grading
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Thanks, Jane. I think Bill's suggestion was very good, as you'd expect, and I am shamelessly plagiarising it for the glossary entry. (I do this with some trepidation since he knows much more than I do about intellectual property rights :) )